Somalia's interim government welcomes a probe into alleged human rights abuses during recent fighting in the capital, Mogadishu, a UN official says.
Mr Holmes cut short his visit after a bomb blast
UN emergency relief co-ordinator John Holmes said although the Somali administration denies any wrong-doing, it will co-operate with investigators.
Some 1,600 people died during fighting between Ethiopia-backed government troops and insurgents in Mogadishu.
The government has declared victory after the worst clashes in 16 years.
Somali's former deputy Prime Minister Hussein Aideed has accused Ethiopian troops of committing genocide since they arrived in December.
They are accused of shelling residential areas as they battled Islamist fighters and clan militias.
The Somali government says the force was needed to install a functioning authority for the first time in 16 years.
"They did not accept any allegations made against them but were nevertheless ready top accept the idea of a visit by the UN high commissioner for human rights, Louise Arbour, and we will organise that in the near future," Mr Holmes said.
Louise Arbour is currently on a tour of DR Congo and may visit Uganda during her African tour.
AU peacekeepers have failed to end the violence in Somalia
Mr Holmes, who cut short his trip in Mogadishu at the weekend due to security reasons, said the UN priority at the moment is to support the African Union mission in Somalia.
Four people were killed when a bomb exploded near the UN compound in Mogadishu while he was there.
"I do not think the devices that exploded on Saturday were aimed at me or the United Nations but I think someone was trying to send a message that the conflict was not over and Mogadishu was not safe," Mr Holmes told reporters in Nairobi.
Up to 400,000 people were displaced from Mogadishu during the fighting and many are living in deplorable conditions outside the capital.
Mr Holmes said the UN has not been able to meet the humanitarian needs of the displaced people due to difficulties posed by insecurity and lack of access.
Relative calm has been restored in Mogadishu and several hundred residents who had fled the city have started to return.
The BBC World Service is holding a special day of programming on Somalia on 15 May