"We have agreed with the Uzbek government to support their efforts and assist tens of thousands, mostly women and children seeking safety in Uzbekistan," it said in a statement.
Ethnic Uzbeks and Tajiks have flocked to the border since the bloodshed, pitting ethnic Uzbeks and Kyrgyz against each other, started on Thursday night.
Fires were raging in the cities of Osh and Jalal'abad on Monday, and some sources said the official figures of 124 people dead and nearly 1,500 injured appeared way too low.
An Uzbek community leader claimed at least 200 Uzbeks alone had already been buried, and the Red Cross said its delegates saw about 100 bodies being buried in just one cemetery.
Charred corpses lay unattended in a burned out ethnic Uzbek shop in Osh and the streets were strewn with shell cases and wrecked cars.
Temir Sariyev, the deputy chief of Kyrgyzstan's interim government, said: "There are local clashes and it is not yet possible fully to contain the situation."
"Armed groups are breaking through here and there and this is linked to the fact that our forces are insufficient" to control events.
Kyrgyz news agency AKIPress said 2,000 people had gathered in the main square in Jalal'abad. It also said 150 to 200 youths were marching around threatening to shoot Uzbeks.
Some accused Kyrgyz government forces of taking part in the mob violence.
Dildor Dzhumabayev, an ethnic Uzbek, said people were gunned down by armed personnel carriers that were used to clear the way for mobs on the streets.
Al Jazeera's Robin Forestier-Walker, reporting from Osh, said witnesses were talking about organised groups being behind the killings.
Different ethnic groups were blaming each other for the bloodshed, he said.
"I get a sense of a city divided, of different communities pitted against each other.
"The Uzbek side always says the military has been involved. And the military is claiming that organised mercenaries took control of some of their vehicles and those are the people who may be causing those disturbances."
There have also been claims that Kurmanbek Bakiyev, the former Kyrgyz president who was ousted in April, has been orchestrating a campaign of ethnic conflict along with his supporters.
Bakiyev, who is in exile in Belarus, has denied any involvement in the violence.
Ban Ki-moon, the UN secretary general, has expressed alarm at the scale of the fighting.
Kyrgyzstan is currently led by a coalition of rival politicians that coalesced earlier this year in opposition to Bakiyev, who was deposed after anti-government protests resulted in deadly clashes.