The quake was centered northwest of Ranau district in Sabah state on Borneo at a depth of 54 kilometers (34 miles), Malaysia's meteorological department said.
Local media said rescuers recovered two bodies from 4,095-meter Mount Kinabalu believed to be of a local guide and a 12-year-old female Singaporean student.
Sabah police chief Jalaluddin Abdul Rahman confirmed two fatalities but couldn't give further details.
Sabah Parks director Jamili Nais said several injured climbers had been brought down the mountain. Most of the 137 stranded people were cautiously trying to descend with the help of park rangers and guides, and some were expected to reach the base camp by early Saturday, he said.
The climbing route was apparently blocked or made dangerous by rocks and boulders loosened by the quake and small aftershocks, Jamili said.
Helicopters were unable to land because of bad weather and the high altitude, he said.
The quake damaged roads and buildings, including schools and a hospital on Sabah's west coast.
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