The leader of the rebel Liberians United for Reconciliation and Democracy(LURD) accused Gyude Bryant, who took office on 14 October, of violating the peace accord in a row over rebel nominations to key administrative posts.
"We want Gyude Bryant to step down. If he does not step down, there wont be UN deployment to LURD areas and we wont disarm," rebel leader, Sekou Damate Conneh said.
Bryant, a low-profile businessman, was picked in August by Liberia's warring factions, to lead the war-ravaged country after former president Charles Taylor was forced into exile.
But barely months after the historic peace accord was signed by various warring factions to end the long running civil war, new differences have cropped up.
"We want Gyude Bryant to step down. If he does not step down, there wont be UN deployment to LURD areas and we wont disarm"
Sekou Damate Conneh
The accord gave Taylor loyalists and the two rebel factions five ministries each in the new transitional government. It said each side had to submit a list of nominees, who could then be confirmed or rejected by parliament.
In a statement published on Thursday, Bryant rejected three nominees put forward by LURD. The statement said those positions were not included in the allocations made in the peace accord.
The rejection has infuriated the LURD rebels.
In a further sign of rising tensions, LURD fighters turned back a UNICEF aid convoy heading out of Monrovia, saying their leaders were being stopped from taking their seats in the new administration.
More than 200,000 people have died in Liberia's civil war since 1989.