Most of the fleeing were ethnic Uzbeks, but there were also reports of Tajiks flocking to the border.
Official figures said nearly 1,800 people had been injured since the unrest started in the city of Osh on Tuesday, with mobs of Kyrgyz men attacking ethnic Uzbeks and torching their houses.
Al Jazeera's Robin Forestier-Walker, reporting from Osh, said the situation there was quiet late on Monday night.
"We've heard sporadic shots ringing out earlier this evening but now it's quiet in the city centre," he said.
"But people on both sides of this increasing divide between the ethnic Uzbek community and the Kyrgyz community are absolutely terrified. People are ready and packed, ready to go at the first sign of trouble or danger."
Witnesses and officials have repeatedly claimed that fighting had not erupted spontaneously between Kyrgyz and ethnic Uzbeks but had been organised by some third party.
Soronbai Jenbekov, the regional governor of Osh, told Al Jazeera: "There are still attempts by third parties to destroy peace between the two ethnic communities.
"But now everyone has realised this and we're working together to stop them. Our forces haven't yet shot any Uzbeks or Kyrgyz – even though both sides are armed."
His comments came after fleeing ethnic Uzbeks accused Kyrgyz government forces of taking part in the mob violence.
Our correspondent said: "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."
Navi Pillay, the UN High Commissioner for Human Rights, urged both Uzbekistan and Tajikistan to "keep their borders open to anyone, irrespective of age or gender, who is in need of sanctuary,
"It seems indiscriminate killings, including of children, and rapes have been taking place on the basis of ethnicity." Her office said in a statement.
"It seems indiscriminate killings, including of children, and rapes have been taking place on the basis of ethnicity."
Navi Pillay, UN High Commissioner for Human Rights
Uzbekistan ordered its borders closed earlier on Monday, saying it could not receive more people.
"Today we will stop accepting refugees from the Kyrgyz side because we have no place to accommodate them and no capacity to cope with them," Abdullah Aripov, the deputy prime minister, said.
The UNHCR said it was preparing to send aid and emergency teams to Uzbekistan.
Several planes arrived at Osh's airport with tonnes of medical supplies from the World Health Organisation on Monday, after reports that stores have been looted and food supplies were scarce.
There have been claims that Kurmanbek Bakiyev, the deposed Kyrgyz president who now is exiled in Belarus, has been orchestrating a campaign of ethnic conflict in the provinces of Osh and Jalal'abad.
The interim government said on Monday it had arrested a "well-known person" suspected of stoking the violence, but gave no other details.
Suspects from Tajikistan, Afghanistan and Kyrgyzstan were also detained and claimed to have been hired by supporters of Bakiyev, Farid Niyazov, a government spokesman, said.
Kenishbek Duishebayev, the Kyrgyz security chief, later said on television that Bakiyev's younger son, Maxim, had been arrested in Britain when he flew into a Hampshire airport on a leased private plane.
Kyrgyzstan's 5.3 million population is mainly made up of Kyrgyz (70%) ethnic Uzbeks (15%) and Russians (8%).
About 50% of the Osh region's 1.2 million inhabitants are ethnic Uzbeks.
About 40% of a population of one million in Jalal'abad region are ethnic Uzbeks.
Prosecutors, who placed him on an international wanted-list in May, alleged that companies he owned avoided almost $80 million in taxes on aviation fuel sold to suppliers of a US air base in the country.
The violent protests that led to the ouster of Bakiyev were fed by anger over corruption permeating his extended family. The interim government, which seized power in April, has vowed to bring them to justice.
The United States called for a co-ordinated international response to clashes.
Hillary Clinton, the secretary of state, had spoken with officials in the interim Kyrgyz government as well as some of the Central Asian country's neighbours to discuss the unrest, Philip Crowley, the state department spokesman, said.
The Kyrgyz interim government has asked Russia to send troops to stabilise the situation in the south, but the Kremlin turned down the request.
Dmitry Medvedev, the Russian president, on Monday condemned the violence and said he had spoken Roza Otunbayeva, the interim president.
He said "tough" action must be taken to prevent further unrest and bloodshed.