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Sumarno, an official in the morgue at Sarjito hospital in Yogyakarta, told Reuters "36 bodies have been brought to the morgue room" there.
In the town of Bantul near Yogyakarta, the local hospital's information officer, Kardi, said: "At least 10 people are dead, hundreds are hurt."
Earlier, a nurse at Muhammadiyah hospital in Yogyakarta had reported at least five deaths there from the quake, which happened just before 6 a.m. (2300 GMT) and had a magnitude of 6.2 according to the U.S. Geological Survey.
The quake's epicentre was offshore but Jakarta earthquake centre official Fauzi said it did not cause a tsunami.