Uzbekistan's president has blamed Friday's unrest in the eastern city of Andijan on what he described as criminals and Islamic radicals.
There have been wildly different estimates of the death toll
President Islam Karimov was speaking for the first time since troops opened fire on demonstrators, killing many.
Thousands of protesters reappeared on the streets of Andijan on Saturday, despite the bloodshed.
About 6,000 people have fled to the border with Kyrgyzstan, sparking clashes with Uzbek police.
The Kyrgyz authorities have closed all border crossings, and officials say many of the refugees are in the large market town of Korasuv.
Several hundred have managed to enter Kyrgyzstan and others are trying to cross illegally.
The BBC's Ian MacWilliam in the Kyrgyz capital, Bishkek, says the situation in Uzbekistan is drawing sympathy in Kyrgyzstan, where large protests brought down the government in March.
The Uzbek government said it was back in control of Andijan on Saturday, but huge crowds were back on the streets, shouting "killers, murderers" and demanding the president step down.
The BBC's Monica Whitlock in Uzbekistan said many people returned to the main square in sympathy for those who died, others seeking news of their missing relatives.
"I'm searching for my son," said one man caught up in the violence on Friday. "I saw people holding up their hands calling 'don't shoot, don't shoot' but they opened fire."
Gardens for graves
The gardens in the square were dug up to make graves for many of the bodies that were left unclaimed in the square overnight.
President Karimov is a staunch backer of the war on terror
Civilians dragged six bodies from an abandoned administrative building, placing them at the foot of a nearby monument to an Uzbek poet.
The Uzbek violence erupted after days of peaceful protest in Andijan over the imprisonment of 23 local business leaders accused of Islamic extremism.
Mr Karimov has described what happened as an armed uprising, planned by Islamic militants linked to the banned Hizb ut-Tahrir movement who wanted to overthrow the government.
He said the leaders of the uprising had been on the phone to Kyrgyzstan and Afghanistan during the siege.
"Their aims are hatred and aversion to the secular path of development. These are unacceptable for us," he said.
But the president denied giving the order for troops to shoot, saying that "no-one gave government forces the order to fire".
Witnesses said troops opened fire on unarmed civilians.
Mr Karimov said about 10 soldiers, and "many others", were killed, but made no mention of protesters being killed.
It is not clear how many died, some people said they had seen at least 200 bodies.
Witnesses said they had seen troops loading dozens of bodies onto trucks.
Hospital officials told the BBC that at least 50 had died and many more were wounded throughout the day.
Mr Karimov, an ally of both Washington and Moscow's war on terror, has taken a tough line on security since a spate of suicide bombings last year, blamed on Islamic extremists.
But critics say the president is using the threat of extremism as a cover to crush dissent.