The 38-year-old was arrested in Kota Kinabalu, capital of the state of Sabah on Borneo island, on charges of causing a public nuisance, The Star newspaper reported on its website. It cited Sabah's state criminal investigation chief Sallehuddin Abdul Rahman.
According to Malaysian law, the punishment for such an offence is a fine of $106.
Read: 11 dead, 8 missing on Malaysian peak after quake: official
The report said the man, arrested at the city's airport as he sought to fly to the Philippines, is believed to have been among a group of 10 foreign tourists who had stripped naked and posed for photos on the summit of the peak on May 30.
The pictures were later posted on the Internet.
Mount Kinabalu, a World Heritage Site and popular climbing destination, is considered sacred by Sabah's Kadazan Dusun tribal group, who believe it is a resting place for spirits. The pictures infuriated many in Malaysia.
On Friday a 6.0-magnitude quake struck near the mountain, sending landslides crashing down from its summit just as more than 150 hikers were at the peak enjoying sunrise views.
Sixteen people have been confirmed killed on the mountain and two remain missing.
In the wake of the disaster, Malaysian social media users and some Sabah officials have focused on the nudists, suggesting that their actions angered the spirits and led to the earthquake.
"This will certainly bring misfortune... we can't play with the spirit of the sacred mountain," deputy state chief minister Joseph Pairin Kitingan had told reporters on Saturday.
It was not immediately clear where the other nine summit nudists were.
Malaysian police spokespersons did not answer calls by AFP seeking details.
Canadian media, citing the country's foreign ministry, had earlier reported that two siblings had been barred from leaving Sabah over the affair.
But Malaysian immigration and police officials have not confirmed this. Officials at the Canadian embassy could not be reached for comment.
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