Liberia's largest rebel faction has demanded that the leader of the power-sharing government step down.
Conneh says Mr Bryant is exceeding his powers
Sekou Conneh, leader of the Lurd group, told BBC News Online that Gyude Bryant was not letting Lurd members of the power-sharing government work.
Mr Bryant was sworn into office earlier this month as part of a deal to end 14 years of civil war.
The BBC's Jonathan Paye-Layleh in Monrovia says this is the biggest threat yet to Liberia's peace process.
"If Gyude Bryant cannot work with us, he must step down or we will pull out from the government," Mr Conneh said.
He said that Mr Bryant had not approved the list of five ministers, submitted by Lurd.
"Gyude Bryant does not have appointing powers, he is an administrator," he said.
Mr Bryant, seen as politically neutral, was chosen to head the new government by two rebel groups, loyalists of former President Charles Taylor and political parties at talks in neighbouring Ghana.
Liberians are desperate for peace
These four groups make up the new power-sharing administration.
Our correspondent says that Lurd ministers are currently working in an acting capacity in three ministries: justice; finance and labour.
However, they are yet to be confirmed by parliament.
Taylor loyalist Daniel Chea is acting defence minister, while Thomas Nimeley, head of the Model rebels has been nominated as foreign minister.
Mr Conneh said he did not have any problem with any of the factions, which signed the accord, just Mr Bryant.
But he said that if the problems continued, the deal would have to be "revisited".
Letter of appointment
Mr Bryant has not yet commented on the allegations but issued a statement on Wednesday stressing that he does have the power to appoint ministers.
Following press reports that Mr Conneh had sent loyalists to take up position not allocated to Lurd under the Accra accord, he also urged civil servants not to let anyone take up executive jobs without an official letter of appointment from Mr Bryant.
Mr Taylor stood down and went into exile in Nigeria as part of the deal, after Lurd forces had entered the capital, Monrovia.
On Monday, one of Mr Conneh's Lurd colleagues George Dweh was elected as speaker of the transitional parliament.
Some 4,300 United Nations peacekeepers have helped bring relative calm to Monrovia but Lurd and their Model allies still control most of the country.