Police in the Somali town of Jowhar, where the transitional government is based, have stopped local UN staff from entering their offices.
The UN children's agency, Unicef, said no reason had been given.
Last week, foreign UN workers left the town because of security concerns after the arrival of some 1,000 troops to support President Abdullahi Yusuf.
The government is divided with several ministers in Mogadishu, refusing to join the president in Jowhar.
Unicef was operating several projects in Jowhar including education, health centres, water, HIV/Aids, youth projects and other humanitarian activities.
Its offices in Jowhar were also the temporary base for other UN agencies.
Reorganisation
Correspondents say the arrival of the troops from Mr Yusuf's home region of Puntland has raised tension, with the Mogadishu groups accusing the president of planning a military offensive against them.
Somalia has been without a functioning national government for 14 years and a transitional parliament, sworn in a year ago, has failed to end the anarchy.
Led by the speaker of parliament, Sharif Hassan Sheikh Aden, more than 100 MPs have set up operations in Mogadishu, but President Yusuf refuses to return there saying it is unsafe.
Mr Yusuf's allies say the troops were part of a reorganisation of armed forces to secure the government's base.
Mr Yusuf had said in July that he would recruit militia forces from his northern stronghold of Puntland to join a new army.
He has little support in Mogadishu and has refused to move there while it is still under the control of his rivals.
The Mogadishu warlords were named as ministers in Mr Yusuf's cabinet but soon fell out with him, siding with the parliament speaker.
Earlier they made threats to attack Jowhar if Mr Yusuf established the government there.
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