The earthquake, measuring 6.6 on the Richter scale, struck near the former Soviet republic's densely populated border area with China on Sunday in the southern province of Osh.
Another 100 people were injured and some 120 buildings were destroyed, as well as roads and power lines.
"The rescue operation at the site of the tragedy is continuing and the figure [the death toll] is not final," a spokesperson for the health ministry said.
The bodies of 25 people have been pulled out from the rubble in the Alaisky district.
Local officials said the earthquake also destroyed the high-altitude village of Nura on Kyrgyzstan's border with China. The area was the epicenter of the earthquake. The village has a population of around 1,000 people.
A total of 38 people, including seven children, have been evacuated from the worst-hit areas by helicopters, the ministry spokesperson said.
The search for survivors and casualties is ongoing, and seismologists have warned that new aftershocks could hit the region this week.
Kyrgyz President Kurmanbek Bakiyev has cancelled all his scheduled events for Tuesday and is expected to visit the affected areas, his spokesperson said. The president has ordered the government to provide aid to the quake victims and deal with the immediate aftermath of the disaster.
Russian President Dmitry Medvedev has sent his condolences to his Kyrgyz counterpart and ordered Russia's Emergency Situations Ministry to provide aid to Kyrgyzstan. An aircraft carrying humanitarian aid to Kyrgyzstan will arrive on Tuesday.
Kyrgyzstan was hit by a series of strong quakes in January and in December 2007. Although a number of buildings were destroyed in the quakes, which reached 6.5 on the Richter scale, no one was killed.