Nigerian forces conducted an unauthorised dawn raid on the UN's main base in the country's conflict-torn northeast on Friday, the UN said, further inflaming tensions between the government and aid groups.

A UN source told AFP that the search of the camp in Maiduguri, known as the "Red Roof", was illegal under international law and may have been triggered by inaccurate information that a key leader of the Boko Haram jihadists was at the base.

"Information about (Boko Haram leader Abubakar) Shekau's presence in the Red Roof was already being spread yesterday on social media," said a memo issued to local staff by the UN's Department of Safety and seen by AFP.

The compound is one of the few safe havens in the region which has been rocked by violence carried out by Boko Haram since it launched an insurgency in 2009.

"At about 2 am early this morning, Nigeria Army troops in trucks are conducting... (a) search on UN Red Roof Humanitarian camp and forced their way into the property," said the internal document.

A witness who declined to be named told AFP that there was a tense two-hour-long standoff between guards at the compound and the Nigerian forces as they sought to enter the base.

- 'Terrified all of us' -

"There were initial fears the armed men were Boko Haram insurgents disguised as soldiers which terrified all of us at the Red Roof," another UN staff member contacted by phone told AFP.

Workers on the base sought refuge in a secure safe room during the search, they added.

The UN team in Maiduguri was ordered to work from home by the security note which warned of possible demonstrations against the organisation and other foreign groups active in the area.

UN secretary-general Antonio Guterres' spokesman Stephane Dujarric said that the organisation had formally complained to the Nigerian government.

"There have been contacts -- we understand from the government that this was a mistake. The raid should not have happened," he said at a daily briefing in New York.

News of the incident came as Vice President Yemi Osinbajo launched a long-planned presidential investigation panel to probe human rights abuses and violations of the rules of engagement by the armed forces.

The judge-led commission represents rare scrutiny of the military by Nigeria's civilian rulers.

The army confirmed that it had conducted several "cordon and search" operations, raiding some 30 premises to locate Boko Haram fighters but denied that it knowingly raided a UN site.

"(Searches) included a property which was said to be occupied by United Nations staff, although the property did not carry a UN designation," the army said in a statement.

Friday's incident happened to a backdrop of strained relations between the Nigerian military and foreign organisations seeking to relieve the humanitarian disaster engulfing the country's northeast.

- 'Cavalier approach' -

In July the Nigerian military blamed foreign aid organisations for a botched bombing at the start of the year on Rann, a northeastern town of 40,000 people, that left at least 100 civilians dead.

Over 20,000 people are estimated to have been killed in the Boko Haram conflict that has devastated northeast Nigeria and become one of the world's largest humanitarian crises.

"There is real fear among us because this incident may turn the same people we are serving against us," said a UN source at the base.

In August 2011, an attack on a UN building in the capital Abuja claimed by Boko Haram left 24 people dead, and in July 2016 the UN temporarily suspended aid deliveries in Borno state after a convoy was attacked.

"The Nigerian army has always had a cavalier approach. They feel that their reputation and their methods have been threatened" by successive amnesties for Boko Haram fighters, said Yan St-Pierre, from the Modern Security Consulting Group.

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