"The protesters are trying to take over the university building and burn it," Otunbayeva said in the capital, Bishkek.
"We condemn all attempts to foment violence and sow the seeds of discord among our people, especially between Uzbeks and Kyrgyz," she said.
"We hope that common sense will prevail and that we shall be able to prevent a conflict."
Stoking racial tensions
The protesters demanded that Kadyrjan Batrov, an Uzbek community leader who they accuse of stoking racial tension, be handed over.
They said Batrov had called for the creation of an autonomous Uzbek district in Kyrgyzstan.
Southern Kyrgyzstan is home to Kurmanbek Bakiyev, the former president who is living in exile.
The interim government blames his supporters for recent violence.
Kyrgyzstan's political revolution on April 7 was the second in five years. More than 80 people died in clashes between protesters and police.
Bakiyev had himself come to power in a popular uprising, the so-called Tulip Revolution of 2005, but became increasingly unpopular amid allegations of corruption and mismanagement.
The interim government has also accused Bakiyev and his allies of election fraud last year and widespread corruption. His Ak-Zol party dominated the last parliament.
Years of under-development and corruption have left many in the former Soviet republic destitute.