African troops in Central African Republic have suspended the hunt for the fugitive warlord Joseph Kony because the new government there is not co-operating with the mission, Uganda's top military official said.

Operations against Kony were put on hold until the mission's status is clarified by the African Union, under whose mandate the forces are deployed in the expansive central African country where rebels deposed a president and took the capital, Bangui, more than a week ago, said Ugandan army chief General Aronda Nyakairima.

"We put a halt to operations until we consult," Nyakairima said. "We're still there and we are going nowhere until we have consulted. We're officially there under the African Union."

About 3,000 African troops, the bulk from Uganda, are currently deployed against Kony's Lord's Resistance Army in Central African Republic, where a former rebel leader named Michel Djotodia has since appointed himself president and announced a new government. The African Union forces are supported by about 100 US military advisers.

Nyakairima said Ugandan troops would stay in Central African Republic until the AU clarifies their status. The AU has suspended Central African Republic's membership and imposed travel restrictions on the country's self-appointed leaders.

Kony, who over the years has taken advantage of weak governments and porous borders to regroup and recruit fighters, would get a lifeline if those deployed to catch or kill him are forced to leave Central African Republic.

It would be a "catastrophe for civilians in the Central African Republic" if the African troops left the country, said Kasper Agger, a researcher with the US-based Kony watchdog group Enough Project.

"A full withdrawal of the Ugandans will also mean that the Americans have to leave as well," Agger said. "All the top commanders of the LRA are in the Central African Republic. That is where the centre of gravity of the operations should be. This will only give the LRA a new safe haven."

Former Central African Republic President François Bozizé was a strong supporter of the military effort to eliminate the LRA. African and US forces use two military bases in Central African Republic for their operations against Kony, an elusive warlord whose precise whereabouts are not known.

Early last year Kony became the subject of a popular online video by the charity Invisible Children, which wanted to bring global attention to his many crimes. The LRA is accused of recruiting child soldiers and taking girls as sex slaves in a brutal campaign for power that originated in Uganda in the 1980s.

Although the LRA continues to abduct children and raid villages in Congo and Central African Republic, the group is not as strong as it once was. Ugandan officials estimate the rebel group's strength at about 250 men, most of them scattered in small groups that are constantly moving in the jungle to elude detection.

Most LRA fighters are operating in Central African Republic, according to Ugandan officials.