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"Special forces and the military were used against civilians in Bishkek, Talas and other places," Ismail Isakov said. "This will not happen in the future."
Although the opposition has previously voiced objection to Manas, Otunbayeva said there were no plans yet to review the lease and her government would meet US diplomats for talks in Bishkek.
"Give us time, it will take time for us to understand and fix the situation," Otunbayeva said.
Officials at Manas were coy Thursday about operations at the base.
"(We at) Manas have taken all appropriate measures to continue to support operations in Afghanistan," said US Air Force Maj. Rickardo Bodden, a public affairs officer. He refused to elaborate for security reasons.
In 2009, Kyrgyzstan said US forces would have to leave Manas, a decision made shortly after Russia granted Kyrgyzstan more than $2 billion in aid and loans. The government later reversed its stance and signed a one-year deal with the US that raised the rent to about $63 million a year from $17 million.
The US is also paying $67 million for airport improvements and navigation systems and another $51.5 million to combat drug trafficking and terrorism and promote economic development.
Leonid Bondarets, who has been affiliated with the Sweden-based Central Asia and the Caucasus think tank, said as long as Bakiyev did not formally resign, there is room for trouble.
"It's hard to predict what is going to happen because Bakiyev hasn't stepped down," Bondarets said in a telephone interview from Bishkek. "The situation is still tense."
The US Embassy denied reports in the Kyrgyz media that US citizens were being evacuated to the Manas air force base, where about 1,200 US troops are stationed. Americans in civilian clothing were seen entering the base Thursday morning.
Russia sent in 150 paratroopers to its base to ensure the safety of the 400 military personnel and their families there, Russian state media reported.
In Bishkek, most of the government buildings in the capital, as well as Bakiyev's houses, have been looted or set on fire and two major markets were burned down. A paper portrait of Bakiyev at government headquarters was smeared with red paint. Obscenities about him were spray-painted on buildings nearby.
Since coming to power in 2005 amid street protests known as the Tulip Revolution, Bakiyev had ensured a measure of stability, but the opposition said he did so at the expense of democratic standards while enriching himself and his family.
He gave his relatives, including his son, top government and economic posts and faced the same accusations of corruption and cronyism that led to the ouster of his predecessor, Askar Akayev.
Otunbayeva blamed Bakiyev for the week's violent clashes.
"Yesterday's events were a response to aggression, tyranny and a crackdown on dissenters," she said. "All the people who were killed and wounded are victims of this regime."
The Health Ministry said at least 74 people were killed and 400 people hospitalized in clashes nationwide Wednesday.
The interim government brings together a wide spectrum of opposition leaders whose differences have undermined them in the past.
One thing they all do agree on - repealing the soaring increases in utility taxes that went into effect in January and have provoked widespread anger.