More than 1,200 people are reported to have been injured but doctors and rights workers have warned the real number of casualties may be much higher because ethnic Uzbeks were too afraid to seek hospital treatment.
Al Jazeera's Robin Forestier-Walker, reporting from the border, said there was a steady stream of ethnic Uzbeks trying to cross and that violence in the city of Osh was ongoing on Sunday.
"We set out into the city earlier today but had to turn back because it was simply too dangerous.
Our correspondent quoted witnesses as saying that three Uzbek neighbourhoods were under attack, but stressed that he had only been able to hear the Uzbek side.
Many of the fleeing ethnic Uzbeks accused Kyrgyz law enforcement officials of abetting gangs of ethnic Kyrgyz.
There has also been claims that Kurmanbek Bakiyev, the former president who was ousted in April, have been orchestrating a campaign of ethnic conflict along with his supporters.
Michael Andersen, a Danish film maker who has been living in Osh, said "it's very likely that Bakiyev and his cronies are behind this".
"I lived in Osh for several years and when you live there, you don't feel any everyday tension between Uzbeks and the Kyrgyz," he told Al Jazeera.
"This is clearly something that is constructed and provoked by some third party."
Bakiyev, who lives in exile in Belarus, has denied any involvement in the violence.
Russia sent hundreds of paratroopers to Kyrgyzstan on Sunday to protect its military facilities in the north, the Russian Interfax news agency reported.
"The mission of the force that has landed is to reinforce the defence of Russian military facilities and ensure security of Russian military servicemen and their families," a Russian military source was quoted as saying.
The interim government has sought Russia's help to quell the violence, but the Russian government has declined the request to send military assistance.
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.
Talaaibek Myrzabayev, the chief military conscription officer in Bishkek, told the Associated Press news agency that Kyrgyz mobs killed about 30 Uzbeks on Sunday in the village of Suzak in the Jalal'abad region.
Ethnic Uzbeks had also ambushed a group of about 100 Kyrgyz men on a road near Jalal'abad and taken them hostages, Myrzabayev said.
Fires set by rioters raged across the city
of Osh and food was scarce after widespread looting.
"The authorities are completely overwhelmed, as are the emergency services," Severine Chappaz, the deputy head of the International Committee of the Red Cross mission in
The south of the ex-Soviet republic used to be the stronghold of the deposed president.
The country 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.
Interim authorities had planned to hold a referendum to approve a new constitution on June 27, but the likelihood of that vote taking place looks increasingly slim.