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.