Elman reaches its figures by tracking fatalities through hospitals and mortuaries.
Accurate casualty figures are difficult to establish because neither side has given an official toll and bodies remain uncollected because of the fighting.
Mohamed Ali, a journalist in Mogadishu, told Al Jazeera that the fighting had spread across the city, growing in intensity throughout the day.
"Sporadic gunfire can be heard from across almost the entire city," he said.
Health workers said that civilians appeared to have borne the brunt of the violence with scores of wounded patients being treated at hospitals across the city.
Husein Gutale, director of Mogadishu's Deynile hospital, said: "So far, we received 51 civilians with injuries and two of them died, a woman and a young boy."
Somalia has not had an effective government since Mohammed Siad Barre was overthrown in 1991.
The Islamic Courts Union seized Mogadishu from the control of warlords in June 2006.
The transitional government, along with Ethiopian troops, defeated the Islamic Courts in late 2006.
About 6,500 people were killed in violence in Mogadishu in 2007.
The 250,000 civilians camped outside Mogadishu are considered to be the world's biggest group of internally displaced people.
Another medical worker told the Reuter news agency: "A mortar shell landed on a house just behind SOS [Save Our Souls] hospital, killing an old man and seriously wounding his wife along with her three children.
"As we were running to help this family, we saw an unidentified dead man lying on the ground."
Sunday's fighting broke out in streets still littered with the uncollected bodies of the victims from Saturday's violence.
One witness said he saw the bodies of four men near the main livestock market, but said that no one had dared to take the bodies away "because the whole place is under Ethiopian siege".
Nur Hassan Husein, prime minister in the interim government, defended the actions of his troops and the Ethiopian military.
"The government is sorry about the fighting and loss of innocent civilian lives," he told a news conference on Sunday.
"We call for peace and are striving towards it, but it is necessary to confront with war anyone that favours violence."
Ethiopian troops helped the Somali military force the Islamic Courts Union movement out of the capital and much of the south of the country in late 2006. They have been deployed there ever since.
Mohammed Gure, chairman of the Somalia Concern Group, told Al Jazeera that the violence was a "popular uprising" against the Ethiopian forces.
"The fighters are not only from the Islamic courts, they are from the Somali nationalists, they come from the former Somali army, they also come from the children and the fathers of those who were displaced or had their homes and livelihoods destroyed by the Ethiopian tanks," he said.
"Somalia is a country under Ethiopian occupation and the Somali people are fighting to free their country."
Mogadishu residents have continued to flee the capital as the government has struggled to impose its authority amid near daily attacks by Islamist fighters and local clans.
Up to 68,000 people are believed to have left since the beginning of the year.