A senior police officer said the school children died when their bus collided with a truck and a minivan late on Wednesday night.
The bus was carrying the schoolgirls from Bali to Yogyakarta when the accident occurred in Situbondo regency, about 830km east of the capital Jakarta.
"There are 52 victims so far. They are the passengers of the bus and were burned to death as a result of the crash," Situbondo Police Chief Tugas Dwi Apriyanto said.
He said bodies, mostly of the girls from a Yogyakarta highschool, had been removed from the wreckage and an unknown number of injured taken to nearby hospitals.
The driver and his assistant survived the crash, although they were badly injured, the police officer said.