The bloodshed has already left 138 dead and more than 1700 people injured since fighting erupted in the city of Osh on 10 June. It spread to the neighbouring town of Jalalabad over the weekend.
Deputy Prime Minister of Uzbekistan Abdullah Aripov says that 45,000 refugees have already been registered, although some estimates put that figure closer to 100,000.
China and Turkey have both sent planes to Kyrgyzstan to evacuate their nationals.
Aid agencies cite eyewitness reports of targeted killings and atrocities in the southern part of the country.
UN Human Rights chief Navi Pillay said she was shocked by the scale of the violence.
“It has been known for many years that this region is a potential tinderbox, and for that reason it is essential that the authorities act firmly to halt the fighting – which appears to be orchestrated, targeted and well planned – before it spreads further inside Kyrgzstan or even across the border into neighbouring countries,” she said.