Kyrgyzstan, a strategically important Central Asian state, houses a key US military base that supplies forces in Afghanistan. Russia also has a base there.
The US embassy in Bishkek and Russia have both expressed concern and called for restraint.
Mr Putin denied Moscow had played any role in the clashes.
"Neither Russia, nor your humble servant, nor Russian officials have any links whatsoever to these events," the RIA news agency quoted him as saying.
A spokesman for Ban Ki-moon said the UN secretary general was "shocked by the reported deaths and injuries that have occurred today in Kyrgyzstan. He urgently appeals for dialogue and calm to avoid further bloodshed".
The unrest broke out in the provincial town of Talas on Tuesday and spread to Bishkek and another town, Naryn, on Wednesday. All three were put under curfew.
One of the poorest of the former Soviet states
Hosts both US and Russian military air bases
Population mostly Kyrgyz but 15% are Uzbek and a significant number of Russians live in the north and around the capital
Kurmanbek Bakiyev has been president since the Tulip Revolution of 2005, which overthrew the government of Askar Akayev
Mr Bakiyev vowed to restore stability but has been accused of failing to tackle corruption
Opponents also complain he has installed relatives in key government posts
Domestic media have come under increasing pressure from the government in recent months
Interior Minister Moldomusa Kongatiyev, who was believed to have gone to Talas to calm the situation, was reportedly severely beaten.
Some reports said he had been killed by the mob, others that he was taken hostage, but there is no confirmation of his fate.
In Bishkek, protesters attempted to storm the president's office but were held back by security forces, who reportedly fired live rounds into the crowd.
Earlier, police had used tear gas and stun grenades to try to break up crowds outside an opposition headquarters but the protesters overcame the police and marched to the presidential offices in the city centre.
Police cars were overturned and set alight and officers attacked by the crowd, some of whom were armed.
Gunfire could be heard crackling through the centre of Bishkek and photographs from the city showed bloodstains on the pavement. The prosecutor's office was also set alight.
Mr Sariyev had been arrested after arriving on a flight from Moscow on Wednesday and a number of other opposition leaders were also detained.
Protesters freed Mr Sariyev on Wednesday and there are unconfirmed reports that up to 10 leaders have now been released.
Mr Bakiyev came to power amid a wave of street protests in 2005 known as the Tulip Revolution, but many of his allies have deserted him claiming intimidation and corruption.
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