The move comes amid fears of reprisals after the International Criminal Court charged Sudanese President Omar al-Beshir with war crimes.
An arrest warrant was issued for Mr Beshir on charges including genocide, crimes against humanity and war crimes.
The AU-UN peacekeeping mission said it would fly out non-essential staff to Ethiopia and Uganda, despite assurances from Sudan that it would protect peacekeepers and humanitarian workers.
Two minibuses carrying UN staff left UNAMID headquarters in El Fasher this morning, en route to the local airport, where the first batch was due to fly to Entebbe in Uganda.
'It's not an evacuation. We're temporarily relocating staff, some non-essential staff. This will probably begin today,' said UN spokesperson in Darfur Josephine Guerrero.
Officials in El Fasher, the capital of north Darfur, said about 200 staff would be flown out today and that further 'relocations' would depend on security assessments.
Staff could return within days or weeks if the mission downgrades its security alert.
