South Sudan President Salva Kiir has accused the UN peacekeeping mission of acting like a "parallel government" in his country.
His comments come after his government accused the UN of hiding rebels and guns at their camps - which it denies.
More than 70,000 civilians are seeking shelter at UN bases across South Sudan after fighting broke out last month.
The UN says both government soldiers and rebels have committed atrocities in one of the world's poorest countries.
What started out as a political dispute between Mr Kiir and his former deputy Riek Machar on 15 December has escalated into full-scale conflict, with reports of ethnic killings.
Around 500,000 people have been displaced and the UN estimates that considerably more than 1,000 have been killed.
The UN is in the process of deploying an extra 5,500 peacekeepers to South Sudan, to bring its forces up to 12,500.
Zero policy towards weapons
The South Sudanese army also says it has recaptured the key town of Malakal after days of heavy fighting, though this is disputed by the rebels.
Friction with the UN followed an attempt on Sunday by the information minister to forcibly gain access to the UN base in Bor, where they believed armed rebels were hiding.
In a statement, UN chief Ban Ki-moon said he was "alarmed" and "disturbed" by the threat to staff of the UN Mission in South Sudan (Unmiss).
"We did not know that when the Unmiss was brought to South Sudan, they were brought as a parallel government with the government in South Sudan," Mr Kiir said.
"They fell short of naming the chief of the Unmiss as a co-president of the Republic of South Sudan.
"If that is the position of Ban Ki-moon, he should make it clear that he wants the UN to take over South Sudan."
Mr Kiir added that the UN should allow the government to search for guns among those seeking shelter in the camps - and hand over any guns, uniforms and government vehicles already in UN hands.