The refugees have been at a camp in Kyrgyzstan since the fled the brutal suppression of an uprising in the Uzbek city of Andijon in mid-May.
Speaking from the Kyrgyz capital Bishkek, Zaccagnini said he could not disclose their destination for security reasons.
"There is currently an ongoing relocation of Uzbek refugees from the south, in Jalalabad, to Bishkek city," Zaccagnini told RFE/RL. "It started this morning. It will be ongoing throughout the day and tomorrow."
Some Uzbek refugees were already awaiting transfer at Bishkek's Manas airport early today. They told RFE/RL's Kyrgyz Service they felt uncertain about their future.
"We don't have any information yet [about where we will be taken]," one man said. "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."
A Kyrgyz airport official said earlier today the refugees were to be flown to Romania.
Nadyrbek Mamyrov, deputy head of the Manas international airport, told Reuters that three out of five planes carrying refugees had arrived in Bishkek from the southern Kyrgyz city of Osh.
He added the refugees would be flown to Romania on a UN-chartered Boeing 747.
The destination, however, could not be confirmed. Other sources suggested the refugees might be traveling to the Czech Republic, Canada, or Ukraine.
Zaccagnini said officials from the country receiving the refugees had urged the UN agency not to disclose its identity.
"We cannot disclose this information for the moment," he said. "The host country has requested that this not be disclosed. So I hope that the media will understand this, and that it is related to security."
Zaccagnini said 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 in May after government troops used force to quell an uprising in the eastern Uzbek city of Andijon.
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.
Observers had warned the refugees risked torture and imprisonment if they returned.
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.
Some 29 refugees had been held in a detention center in Osh, and faced immediate deportation.
Zaccagnini of the UNHCR said most of those men are also due to be sent out of Kyrgyzstan and sent to a third country.
"We hope that the ones that have been mandated refugees -- which is 25 of the 29 -- will also be relocated together with the larger group," he said.
Some Uzbek refugees at the Manas airport say they feel free to criticize the Uzbek regime of President Islam Karimov only when they are outside Uzbekistan.
"We don't know yet how long we will be here [at the airport]," one man said. "Some people say we will have to wait until everybody else arrives here [from the camp]. We've been able to breathe freely since we came here to Kyrgyzstan. We hope everything will be good in Uzbekistan. Until then, we don't know what it is going to happen to our lives."
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 an operation to suppress "a terrorist action" orchestrated by "foreign forces."
Human rights groups say as many as 750 people may have been killed.Related Story:
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For RFE/RL's full coverage of the Andijon uprising and its aftermath, see "Unrest In Uzbekistan"