When he appeared on a local radio talk show last week, President Yoweri Museveni warned religious leaders against making political statements.
In his caution, specifically shot in the direction of the bishops, Mr Museveni indicated that the clerics, just like traditional leaders and soldiers, are specifically prohibited from active politics.
This statement has since attracted public disapproval from clerics of all calls as well as scholars and the general public.
Considering the cordial relationship hitherto enjoyed by the church and the present government, specifically Mr Museveni over the last 17 years, this seems like a red line that could mark the start of a sour relationship.
The dissent in opinion and position definitely comes after proposals by the ruling Movement government to amend Article 105 (2) of the constitution on presidential term limits - now referred to as the "third term" or mischievously, the "sad term."
So is the church coming out bold and clear against Mr Museveni?
The first shot
In an interesting feud that is bound to rage on, the bishops fired the first shot on 2 June when the Uganda Joint Christian Council (UJCC), after a plenary meeting at Pope Paul Memorial Centre in Kampala, issued a terse statement opposing the third term. UJCC brings together all major Christian churches in Uganda.
Said the statement: "It was noted that the expressed desire by a section of Movement supporters advocating for abolition of term limits for the president does not reflect well on the commitment to building a democratic culture and should therefore be discouraged. The Uganda we want must be founded on the spirit of constitutionalism and the rule of law."
That was not enough. The statement also touched on the sensitive subject - making it clear that it is incumbent upon President Museveni to prepare for a smooth hand over of power in 2006.
Coincidentally, the statement came soon after the chairman of the Catholic laity and also minister of State for Privatisation, Prof. Peter Kasenene's infamous contradictory remarks against his church superiors.
Mr Museveni's categorising of religious leaders and soldiers, during the Capital Gang talk show, followed this controversial statement.
His political assistant, Mr Moses Byaruhanga, says church leaders are intervening in a constitutional matter, which could divide their flock.
Mr Byaruhanga has actually accused the bishops of meddling in politics and advised them to help the souls of their flock, just as his boss did.
The message from Mr Museveni and company to the church leaders is clear; can you keep on the sidelines?
And the clerics are saying NO
The clerics are replying with a specific no to Mr Museveni's attempts to suppress them.
"Those saying that the church should keep out of the political debate are mistaken," Rev. Fr. Lawrence Kanyike said.
Fr. Kayike said the church must intervene when it discovers that the politics is intending to oppress the people.
The Rev Fr argues that the church plays a prophetic role. "The church is the voice of the voiceless," he says.
Mbarara Catholic Archdiocese vicar general, Msgr Edward Benign-Muntu backs Fr. Kanyike. "I find it strange for any one to say that the church should not meddle in politics! The church indeed does not meddle in politics at all. The Church is not a foreign entity in Uganda. The church has a community of believers, which includes its leaders, all of who individually and collectively; have civic rights and duties in their own country," Fr Muntu told Sunday Monitor in a separate interview.
Fr. Kanyike resists calls that the church should search for the souls of their flock. "We cannot dichotomise the human being into soul and spirit. The church doesn't speak to spirits, it speaks to people," he said.
He intimates that in the present particular case, when the incumbent power suggests a constitutional amendment to the presidential term limits, it insinuates that the incumbent president is an interested party to which the church is saying no.
"Unfortunately history in our country has been that when the church supports a government programme, then it's alright, but when it opposes then they have meddled in politics," Fr. Kanyike says, a view shared by Rev. Canon Grace Kaiso, the Secretary General of UJCC.
"What is clear is that when the church intervenes, it is not interested in taking power, we have a mutual responsibility to the people of Uganda," Rev. Kaiso told Sunday Monitor in a separate interview.
History of Church intervention in Uganda's politics
In 1962 shortly before independence, Bishop Joseph Kiwanuka advised the Baganda not to involve the Kabaka in politics.
The Baganda, who unsuspectingly accepted trickery at the hands of Dr. Milton Obote (and the Uganda People's Congress UPC) went against the bishop's advice.
The crisis that engulfed the country in 1966 forced Kabaka Edward Mutesa II into exile. He was brought back in a coffin several years later.
In the entire history of Uganda the church leadership, of the main denominations, has remained in dialogue with government leaders to ensure that justice and peace prevail. Even in days that were regarded as most dangerous, Bishops' Conferences did not succumb to intimidation; even if they wanted to, their flock kept pressing them to use their position and say something.
It was not easy and sometimes the price was very high, including harassment and arranged accidents for people who were labelled vocal.
In 1997, before the fall of Amin, bishops issued a statement, which kicked the process that weakened that terror regime.
The bishops were reacting after the murder of Archbishop Janan Luwum, which was preceded by the fleeing of another bishop, Rt. Rev Festo Kivengere into exile.
The late Emmanuel Cardinal Nsubuga selflessly and fearlessly spoke against dictatorship during the Amin and Obote II era.
In fact the late cardinal is widely believed to have enormously contributed to President Museveni's bush war.
So what is new with the bishops making political statements and the president's calculated move to stop them?
"I must point out that when you do not hear complaints from politicians about the church, most likely it is because what church leaders are doing and saying is working in favour of politics. But when the prophetic duty of the church demands that certain comments be made - which politicians regard as likely to require drastic change in the status quo - then you hear this call for church and state dichotomy," Msgr Muntu says.
Fr. Kayike says that actually had Cardinal Nsubuga been alive today, President Museveni wouldn't be making such statements.
"He would be afraid to make such a statement but probably because we his successors are not vocal, or we have given him too much benefit of doubt, he has taken our silence as a weakness," he said.
What the others say
A Makerere University law professor, John Jean Barya says the church should be part of politics.
"It's not a question of intervening, they (church) should have a say," he said.
Prof. Barya says attempts by President Museveni to divert their current position are not only contradictory but also self-serving.
"For cultural leaders, the issue is constitutional, but as far as I am concerned, there is no constitutional provision that prohibits church leaders from making any political statement," he said.
But President Museveni's assistant on research and information, Mr Frank Tumwebaze, says he would support the idea of the Church confining itself to general principles of love, peace and unity. He says it should avoid taking positions on highly contested political issues.
"For example, if the Church says they don't support the lifting of the presidential terms as they have indeed expressed, how are they going to cater for the political interests of some of their followers that favour the lifting? Where will the harmony be in this case?" he asks.
"Such politicking also will be endangering the Church, because it will be expected to take a position on every political matter. For example I will ask, what is the position of the Church on federo, or Obusinga (for the Kasese people)?" he says.
Church people working in political positions
Prof. Barya said that it is President Museveni who is the champion of using church people politically - even in the bush days.
As a result there are many church people in government positions, with some specifically appointed by President Museveni.
Some of the high profile ones include Sr Margaret Magoba, the deputy chairperson of the Electoral Commission and Fr. Albert Byaruhanga, a presidential assistant.
Says Prof. Barya "When they [church leaders] support him [Mr Museveni], its OK, when they oppose him its not."
But Mr Byaruhanga, President Museveni's political assistant says church leaders working in government are appointed with specific permission from their churches. He notes that even then, they would serve in non-confrontational institutions like the EC.
Msgr Muntu says however that there are not many priests involved.
He says he is aware that even those few appointments were in done in light of special request and arrangements that were initiated by politicians. Why did the state allow such arrangement to go on? Why are the same quarters now urging for total separation of church and state interaction".
Was the church in Uganda silent in the last 17 years?
There is no doubt that President Museveni was the darling of the churches when he assumed power in 1986. He brought the Catholics on board and the Anglican Church, in his nation building project.
For their good co-operation, the president would give every new bishop a Mitsubishi Pajero and half a dozen heifers upon consecration. It became so normal that when a Luwero bishop was given a small Daewoo car instead of a Pajero, he protested.
Giving bishops trinkets and appointing religious leaders into political positions has been a hallmark of President Museveni's regime. This at one time became a big concern to many observers as the bishops and church leaders were seen to be jumping into bed with government.
"If you see a bishop or sheikh driving a new Shs 60m ($40,000) Pajero in Uganda today, you know it was donated to him by President Museveni. Many bishops and priests are falling over themselves to please the president and get a car or money," Charles Onyango-Obbo, former Monitor managing editor wrote in his column in The East African, 20-26 March, 2000.
However, the church says it was not silent.
Msgr Muntu says the church was actually supportive of the Movement government in reconstruction programmes.
He said the church objected to the Movement's attempts to undermine religion by portraying it negatively in the syllabus of the Chaka-Mchaka (political education) courses and challenged the charge that religion was a factor in underdevelopment and social conflicts. Subsequently a balance has been struck.
"The reconstruction of structures and rehabilitation of human minds in Uganda, which had been adversely affected by past regimes, was not a single-handed achievement of the Movement government; the church played a significant role," he said.
"That some bishops received gifts from the Head of State: I have no problem with people giving and receiving gifts. Such is a normal African and indeed a global cultural practice. It is up to the giver and receivers to know what implications are involved," Msgr Muntu says.
He denies there has been church silence on the issue of political pluralism for the last 17 years.
"What if the signs of the time had not called for any serious exchange about the topic? What if other players and interested parties on the issue were handling it at the rate and prudence that was generally on course! Would the church have to speak for the sake of it?" he asked.
He said the Catholic Church has a specific Commission of Justice and Peace in every diocese, which has done all within its power not only to denounce forms of human rights abuse, but also to try and equip citizens with the right tools of knowledge for defending their rights.
"There are several occasions when government leaders have been put to task by the church to check certain abuses in various parts of Uganda. May be because the approach was non-confrontational that is why you may not know them," he said.
So what's the way forward?
"We raise these issues not because we have lost faith in the present government or the president. We are trying to lay a foundation for a culture of peaceful transition that is basic for the stability and the viability of the country, says Rev Canon Kaiso.
Fr Kanyike says that given the fact that the present government has been riding on shoulders of a terrorised population, it was time for the church to take up its role as spokesman.
"The present electorate does not vote out of concern but out of fear of violence. Given that the government in power has a military stigma, its time for the church to intervene," he said.
Fr Kanyike says that Uganda has reached a very difficult position where there is need for honesty between the church and government.
Prof. Barya backs the religious leaders.
"Its good that they have taken a common position. Given that it has not been easy in the past," he said.
"Given that the majority population in Uganda is peasantry, civil society is weak and the political parties have of course been undermined, only the church remains as the most organised institution. It's important that they continue playing that role," he said.
Prof. Barya said for the church to be effective, its important they sensitise their flock about the positions they are taking and continue upholding them and resist attempts by government to intimidate or divide them.
But Mr Byaruhanga says the church is unnecessarily meddling into an issue that is being handled through a constitutional process.
Will his boss listen to the ringing bells from the church leaders?