More than 5,000 protesters packed a stadium in the north of Mogadishu, burned an Ethiopian flag and carried signs that said, "We Must Fight Them!"
Ethiopian and Somali government officials have denied that Ethiopian soldiers are in the country, but witnesses in several towns reported seeing them crossing the border four days ago.
Addis Ababa has said it will protect the largely powerless interim government in its base in the town of Baidoa and threatened to "crush" any attack by Islamic fighters.
The protests were organised by the Union of Islamic Courts which has taken control of the capital and much of the south of the country from regional warlords.
On Sunday, a top Islamic leader, Sheikh Sharif Sheikh Ahmed said, "I call on Somalis to be ready for a holy war against an invasion from the enemy of the religion and the country."
Several Somali MPs have also called for the Ethiopian soldiers to leave.
The statement from 16 Somali MPs is the first time people within the interim government have admitted that Ethiopian forces have crossed into the country.
"Ethiopian troops should get out of Somalia as soon as possible and should cease from the constant aggression against Somalia," the statement said.
Ethiopia has threatened to
'crush' the Islamic fighters
"This move is a clear interference against the freedom and sovereignty of Somalia," it added.
The MPs urged the international community to put pressure on Addis Ababa to withdraw its troops to prevent further insecurity in the Horn of Africa region.
Some of the MPs responsible for the statement are believed to be Islamist sympathisers based in Mogadishu.
Earlier, a Somali warlord, who was one of a group which fought against the Islamic militia for control of the capital, offered his support to the government.
Mohamed Qanyare Afrah arrived in Baidoa with 150 militiamen and eight pickups mounted with machine-guns, the main mobile weapon in Somalia.
Prime Minister Ali Mohamed Gedi had fired Qanyare from the cabinet as he had fought against the Islamic group independently of the government.
But on Monday Qanyare, the former national security minister, was welcomed by members of the transitional parliament and local administrators.
Somalia has not had an effective central government for 15 years since warlords overthrew Mohamed Siad Barre in 1991 and then turned on each other. Some of those warlords now sit on the transitional government.