The 6.0-magnitude quake struck near the mountain around 7:15 am, jolting a wide area of the Malaysian state of Sabah on Borneo island, causing widespread but relatively minor damage.
No deaths had been reported as of late afternoon.
But Sabah state tourism minister Masidi Manjun told AFP the quake had triggered landslides and sent huge boulders tumbling down the 4,095-metre mountain's wide granite crown.
Around 160 people including foreigners were stuck just below the picturesque summit, unable to descend due to lingering danger from rockfalls and because a key trail had been cut off, Masidi said.
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Authorities had earlier said more than 200 were feared trapped but Masidi said some appeared to have made it down.
State officials were quoted by the New Straits Times saying at least four climbers had suffered injuries including broken bones and head wounds due to falling rocks.
The tremor's force was so strong that it snapped off one of the two large "Donkey's Ear" rock outcroppings that form a distinctive part of the peak's craggy profile, Masidi said.
Kinabalu's broad but steeply undulating moonscape-like summit is often lashed with heavy rain, and night temperatures can dip below freezing despite the tropical latitude.
The US Geological Survey said the quake struck at a depth of 10 kilometres, with its epicentre located about 54 kilometres east of Kota Kinabalu, the capital of Sabah.
No tsunami warning was issued and there were no initial reports of major damage.
Colin Forsythe, a resident of Kota Kinabalu, said the quake lasted around 15 seconds and felt "as if a truck had crashed into a brick wall".
Thousands of people complete the relatively easy climb of Mount Kinabalu each year. Malaysian national schools currently are on break and the peak was busy with visitors at the time of the tremor.