But she said Bishkek has told the UNHCR that none of the 29 will be returned.
"We have taken up the issue with the Kyrgyz authorities and we've received full assurances that the 12 people that they are asking for will be able to proceed to Bishkek just as planned. The presence of the Uzbeks will not affect this decision. So, we've received full assurances," van Genderen Stort said.
The UNHCR believes that 25 out of the 29 should be released and relocated together with the larger group of refugees being relocated. The four remaining detainees are not part of the 12 whose return was requested by the Uzbek authorities.
"We have an agreement [with Kyrgyz authorities] for 25 of the 29, and these other four are not part of the 12 that the Uzbekis asked for. We are still discussing the other four that are remaining," van Genderen Stort said.
The 29 men were detained earlier this month at Uzbekistan's request for suspected criminal activities and faced immediate deportation. They entered Kyrgyzstan in May as part of a wave of hundreds of Uzbeks fleeing Uzbekistan following an uprising and a military crackdown in the eastern Uzbek city of Andijon.
Four refugees were extradited to Uzbekistan in June. Uzbek authorities have continued to pressure Bishkek to hand over several other refugees, who they say are guilty of terrorism and other crimes.
Observers have warned that refugees risked torture and imprisonment if they are returned.
The UNHCR announced earlier today that over 400 Uzbek refugees are being sent to a third country.
Carlos Zaccagnini, the head of the UNHCR mission in Kyrgyzstan, spoke to RFE/RL from the Kyrgyz capital Bishkek, and said he could not disclose their destination for security reasons.
"There is currently an ongoing relocation of Uzbek refugees from the south, in Jalal-Abad, to Bishkek city. It started this morning. It will be ongoing throughout the day and tomorrow," Zaccagnini said.
Some Uzbek refugees were already awaiting transfer at Bishkek's Manas airport early today. They told RFE/RL they felt uncertain about their future. "We don't have any information yet [about where we will be taken]. In such a difficult situation, it is better to go to a third country than to Uzbekistan. We have to go where they send us," one male refugee said.
A Kyrgyz airport official, Nadyrbek Mamyrov, said earlier today the refugees were to be flown to Romania.
Van Genderen Stort of the UNHCR denied this.
"The information about a Boeing 747 going tonight to Romania is false. They won't leave until -- I mean, the earliest will be Friday morning [29 July]," van Genderen Stort said.
Other sources suggested the refugees might be traveling to the Czech Republic, Canada, or Ukraine.
The UNHCR’s Zaccagnini said the country receiving the refugees had urged the UN agency not to disclose its identity adding that the country is to be a temporary base only for the refugees. From there, their status information will be processed and they will be sent to their final destination.
Some 450 Uzbeks fled to neighboring Kyrgyzstan last May after government troops used force to quell an uprising in the eastern Uzbek city of Andijon.
The UNHCR has urged third countries to grant asylum to the Andijon refugees, who had been stranded in a camp near the Kyrgyz-Uzbek border. The UN and rights groups had feared Uzbek authorities might try to seize the refugees and force their return.
Hundreds of people, including many women and children, were killed in Andijon on 13-14 May. Witnesses said government troops and security forces shot into a crowd to put down an uprising.
The Uzbek authorities say 187 people -- mostly "terrorists and extremists" -- were killed in what they say was "a terrorist action" orchestrated by "foreign forces."
Human rights groups say as many as 750 people may have been killed.