The 6.0-magnitude quake struck near the mountain around 7:15 am, jolting a wide area of the state of Sabah on Borneo island, causing widespread but relatively minor damage.
No deaths had been reported as of late Friday 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.
“Its very tricky now. We can’t land a helicopter up there because visibility is so bad, but the people can’t come down on their own because the main route is now impassable,” he said.
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 force of the tremor 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.
He said authorities were now focused on trying to get supplies including food, water and warm clothing to the stranded climbers in anticipation of a possibly wet and chilly night.
Kinabalu’s broad but steeply undulating moonscape-like summit is frequently 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 state capital Kota Kinabalu.
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.
Residents in the area reportedly fled in panic from homes and buildings, including Kota Kinabalu’s International Airport, and social media users uploaded photos of damaged roads, shattered storefront windows, and cracked walls.
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.
Most climbers attack the peak early in the morning after overnighting at a resthouse perched at 3,270 metres above sea level, descending a short time after, so they typically do not take food or camping equipment to the peak.
Authorities have closed the picturesque mountain, a major tourist draw, until further notice.
Strong earthquakes are rare in Malaysia, which lies just outside the Ring of Fire, the belt of seismic activity running around the Pacific basin.
Mount Kinabalu is sacred to the local Kadazan Dusun tribal group, who consider it a resting place for departed spirits.
A group of 10 apparently Western men and women tourists angered locals last weekend when they snapped nude photos at the summit and uploaded them on to the Internet.
Some Malaysian social media users posited that the quake was a sign the spirits had been angered by the act.