Some 400 others were airlifted to Romania last week
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Kyrgyz authorities say they intend to return 15 Uzbek refugees, despite UN concerns that such a move could violate international conventions.
The Kyrgyz general prosecutor's office said it had "reliable evidence" the men were involved in serious crimes.
The decision comes just days after the UN flew nearly 440 other Uzbek refugees out of Kyrgyzstan to Romania.
On Monday Uzbek officials denounced the airlift as "unacceptable and outrageous interference" by "outside forces".
'Prison escapees'
The 15 refugees Kyrgyzstan wants to deport back across the border to Uzbekistan are currently being detained in the southern Kyrgyz town of Osh.
Uzbekistan wants the men back in the country to face allegations they helped organise an uprising in Andijan in May.
Kyrgyzstan's deputy prosecutor general, Nurlan Jeenaliyev, said that 12 of the 15 had escaped from a prison in Andijan when anti-government protesters took over the town.
Eleven of them are accused of terrorism and membership of a banned Islamic group, Akramiya, while three others are accused of killing Andijan's prosecutor, Mr Jeenaliyev told the French news agency AFP.
"We are continuing to investigate them. The Uzbek prosecutor general's office has sent us documents from the criminal investigations opened against them," he said.
But Mr Jeenaliyev also said he would talk to the UN High Commissioner for Refugees about the case, as some of the 15 accused men had already received official refugee status.
UN Secretary General Kofi Annan has appealed to Kyrgyzstan's government "to strictly abide by its international obligations in the treatment of asylum-seekers".
The UN and international human rights groups fear that, if handed back to the hardline Uzbek authorities, the 15 refugees could face torture or even execution.
The UN says torture is systematic in the Uzbek judicial system, and human rights groups say several thousand people in Uzbek jails are there because of their religious or political views.
Border camps
The 15 men - together with more than 400 others - fled eastern Uzbekistan in the immediate aftermath of the Andijan uprising in May.
The Uzbek government claims 187 people were killed in the violence, which it blames on Islamic extremists and criminals.
Before flying to Romania, the refugees lived on the Kyrgyz border
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But eyewitnesses say up to 500 people were killed when troops opened fire on protesters, among them women and children.
The refugees fled across the border to Kyrgyzstan, where the majority have spent the last few months living in camps until they were flown to Romania late last week.
They will stay there temporarily before being resettled in other countries - believed to include Canada, Germany, Australia and Scandinavian nations.
The Uzbek foreign ministry said on Monday that the airlift was in breach of "all procedures and norms of international law", and that "unprecedented pressure" had been applied on the Kyrgyz authorities not to send back the refugees.
"This was an unacceptable, crude interference by outside forces," it said in a statement.