Witnesses said civilians were among the dead, some with their throats cut
Ethiopia has denied accusations from Amnesty International that its troops killed 21 people at a mosque during the recent fighting in Somalia's capital.
Government spokesman Zemedkun Tekle dismissed their report as "mere hearsay and propaganda" coming from Islamists.
Amnesty International said the soldiers also took away 40 children during the raid on the al-Hidaya mosque.
The UN emergency relief co-ordinator John Holmes has called for action against those involved in the attack.
Some 80 people were killed this week during fierce fighting between Ethiopian backed government troops and insurgents in Mogadishu.
Six of the dead are religious leaders from the Tabliq Sufi sect, which is not involved in the conflict.
"Amnesty's allegations are unsubstantiated lies and propaganda that they have received from Islamic groups in Somalia," Mr Tekle told Reuters news agency.
The injured were taken to hospitals after the fighting, but many fled
Mr Tekle said their troops were not involved in such incidents.
But UN humanitarian chief John Holmes said there has been an increasing trend of indiscriminate use of force against civilians by all parties in the conflict in contravention of international humanitarian law.
"Those who are responsible include members of recognised armed forces who should be held accountable for their actions," Mr Holmes said.
The recent fighting is threatening plans for reconciliation talks between the interim government and the Somali opposition alliance which includes the Islamists.
Islamist leader Sheikh Sharif Sheikh Ahmed has told the BBC Somali service they are reconsidering their earlier stand to hold talks with the government.
Reports from neighbouring Djibouti where the talks are due to take place, say UN special envoy for Somalia Ahmedou Ould Abdalla has been holding talks with representatives of the alliance in a bid to rescue the situation.
There is also an impending humanitarian crisis in the country after relief agencies reduced their presence in most parts of the country due to increasing insecurity, the UN says.
It estimates some 750,000 residents of Mogadishu have fled the city in the past year following the violence.
The Ethiopians intervened in 2006 to help government forces oust Islamists who had taken control of much of southern Somalia.
The country has not had an effective national government since 1991.