The renegade general who last week seized the Democratic Republic of Congo town of Bukavu says he will return, unless attacks on his ethnic group end.
Nkunda denies taking orders from Rwanda
Brig Gen Laurent Nkunda says that following the withdrawal of his forces, the Banyamulenge community has been targeted for reprisals.
But a UN spokesman denied that there had been a big backlash.
The fighting in and around Bukavu has posed a serious threat to DR Congo's complex power-sharing arrangements.
The Congolese government has issued a warrant for Gen Nkunda's arrest.
The Banyamulenge are Congolese Tutsis, who retain links to their Rwandan kinsmen.
Gen Nkunda said that he had captured Bukavu to end a genocide of the Banyamulenge, led by the army.
He withdrew, acknowledging that there had been no genocide and under pressure from the international community to pull out.
"I think this is going to disrupt the entire peace process because now the situation in Bukavu is worse than before," he told Belgian radio.
UN spokesman Sebastien Lapierre told BBC News Online from Bukavu that on Wednesday, there had been "targeted looting of those seen as dissident collaborators" and peacekeepers had been deployed to the Nguba district, where Banyamulenge live.
He said that the house of one of Gen Nkunda's allies, Col Jules Mutebusi, had been burnt down but "everything was now returning to normal."
The new civilian governor is due to arrive in Bukavu later on Thursday, he said.
About 1,000 Banyamulenge have fled to Burundi from the Congolese town of Uvira, south of Bukavu.
"They told us that they were threatened by people of Uvira from other tribes," local official Louis Niyonzima told Reuters news agency.
Nkunda says he acted to protect the Banyamulenge ethnic group
On Wednesday morning, thousands of Bukavu residents lined up to cheer the return of government troops.
Congolese President Joseph Kabila accused Rwanda of being behind the rebellion but this was denied by Rwanda.
Gen Nkunda is based in Goma, from where he led his men to take Bukavu, but his present whereabouts are unknown.
He is a member of the Congolese Rally for
Democracy (RCD), a former rebel group backed by neighbouring Rwanda.
Under a deal to end five years of war in DR Congo, the RCD and other rebel groups joined a power-sharing government.
Their troops are supposed to be integrated into the DR Congo's new national army.