The government said security forces acted to restore order and it did not have casualty figures. The government also said the demonstrations were illegal and that organizers would be dealt with sternly.
The head of the European Union observer mission said some opposition politicians had been placed under house arrest.
"The mission has conveyed to the government its condemnation of the home arrests and other harassment and threatening measures imposed on the opposition coalition ... leaders in the last days, severally curtailing their political activities and personal movement," Ana Gomes said at a news conference.
She said the EU mission expressed its "deep concerns about the dangerous situation Ethiopia is now facing."
The protests have erupted despite Prime Minister Meles Zenawi's move to ban demonstrations immediately after the May 15 legislative election. Meles' party won a majority of seats in the election, according to official results. Opposition parties say there was widespread fraud and intimidation, charges the ruling party denies.
The elections had been seen as a test of Meles's commitment to reform his sometimes authoritarian regime. Before questions surfaced about the count, EU observers had called the campaign and voting "the most genuinely competitive elections the country has experienced," despite some human rights violations.
Wednesday's shooting began after soldiers arrived at the central business district where protesters were throwing stones.
One of the injured, who refused to give his name because of fear of retribution, said the army fired on fleeing people. He said he was caught up in the protests, and was not taking part in it.
The Addis Ababa city police also shot at protesters, said another person lying on a hospital trolley after emergency treatment.
"The police were running at the crowd, firing shots. I got shot in my leg," the 22-year-old day laborer who identified himself by one name, Getu, said. "I was just trying to get home to avoid the trouble."
An Associated Press reporter saw 11 bodies in the capital's main hospital, at least four with gunshot wounds to the head. Doctors at two others hospitals reported an additional 11 dead and hundreds of injured.
A police statement issued Wednesday evening said only 13 people were killed and 40 injured. The police also said demonstrators tried to steal their weapons.
"Today, some of their followers — and some who wanted to use this opportunity for looting — have gathered in some parts of Addis and disrupted the smooth functioning of life. So the government had to use the anti-riot police to resolve the situation," he said, adding that seven buses were destroyed and businesses and banks were damaged.
Bereket rejected claims the police used excessive force.
The two main opposition groups, the Coalition for Unity and Democracy and the United Ethiopian Democratic Front issued a joint statement demanding an end to the violence.
"These murderous acts have resulted in the killing and wounding of a large number of innocent Addis Ababa citizens, including women and underage youth," the statement said.
The leader of the Coalition for Unity and Democracy, Hailu Shawel, said police tried to place him under house arrest, but he climbed over a back fence before they could seal off his home. His deputy, Berhanu Nega, said he was being followed by security personnel.
State-run radio broadcast a warning in Amharic to Ethiopians not to stage more protests.
"With effect from today, especially after the issuance of this statement, the police and security forces will take stern action against those shouting in groups, trying to cause destruction of government and people's property and piling stones on the roads and trying to disrupt peaceful and legal movement of the people," the warning said.