Uzbekistan's chief prosecutor has said 169 people died in clashes in the town of Andijan last week, but he denied security forces had killed civilians.
Andijan has been under a curfew since the weekend
An Uzbek military source has however told the BBC that the true death toll is more than 500, with many more injured. He spoke of a "massacre".
Some Uzbeks believe bodies are being released slowly to keep the death toll in doubt, a BBC correspondent reports.
The US and UK have condemned the violence and urged political reform.
Moscow has reacted officially for the first time to the events in Andijan, echoing Uzbek President Islam Karimov's assertion that Islamic militants were to blame for the violence.
However, Russian Foreign Minister Sergei Lavrov acknowledged that "a great many completely innocent people" had died in Andijan and he expressed "profound regret".
Troops moved into Andijan on Friday soon after protesters stormed the town's prison and freed 23 suspected Islamic extremists, who then joined a public rally in the centre.
The town has been under curfew since the weekend.
"Only terrorists were liquidated by government forces," said Prosecutor-General Rashid Kadyrov, adding that 32 members of the security forces also died.
"Not a single civilian was killed by government forces there," he told reporters, and described as "absolutely absurd" reports that troops had fired on peaceful demonstrators.
Most populous central Asian former Soviet republic, home to 26m people
Ruled since 1991 independence by autocrat Islam Karimov
Accused by human rights groups of serious abuses, including torture
Rocked by violence in capital Tashkent in 2004
Government says radical Islamic groups behind violence
According to Mr Kadyrov, gunmen killed three women and two children.
Reports of a much higher toll were "willing misinformation put out by the international community", he said.
The military source who spoke to the BBC said he had come forward because he wanted the world to know what really happened.
The BBC's Monica Whitlock notes that Uzbekistan is a tightly controlled state in which officials almost never speak to journalists and invariably state the government line.
That a military figure should break silence on such a vastly important and sensitive issue is unprecedented, she adds.
According to an Uzbek opposition party, 542 people were killed in Andijan on Friday and 203 others on Saturday in Pakhtabad, another town in the Fergana Valley.
Nigara Khidoyatova, leader of the Free Peasants Party, told the Associated Press news agency her party had arrived at the figure by speaking to relatives of the dead.
President Karimov dismissed her figures as a claim made by a "person who needs psychiatric treatment", AP adds.
Witnesses who spoke to the BBC earlier said security forces had shot at civilians, including women and children, though a doctor who saw bodies collected afterwards said most of the dead appeared to have been adult men.
Neighbouring Kyrgyzstan has registered more than 500 refugees from Andijan. Some said troops shot at them as they tried to cross the border and that some died.
The London protesters may be charged with criminal damage
The US said on Monday it is "deeply disturbed" by reports from Uzbekistan that troops fired on unarmed civilians.
Since events started unfolding on Friday, Washington has been under pressure to take a tough line against the Uzbek regime, a key US ally.
On Tuesday, about 30 protesters gathered outside the US embassy in the capital, Tashkent, to condemn Mr Karimov as a "killer of the people".
In London, police arrested 37 people outside the Uzbek embassy there after demonstrators daubed the building with red paint.
A member of the Islamic group Hizb ut-Tahrir told the BBC the protest was a "show of solidarity with Uzbek Muslims".