The boat is believed to be the third bound for Malaysia stopped in Myanmar waters since monsoon rains began to subside last month, bringing calmer weather, raising fears of a fresh wave of hazardous voyages after a 2015 crackdown on people smugglers.
Moe Zaw Latt, director of the government office in Dawei, a coastal town in southern Myanmar, said fishermen had reported a “suspicious” boat to authorities.
The navy stopped the boat on Sunday and detained the 93 people, who said they had come from the Thae Chaung camp in the Rakhine State capital of Sittwe, he said.
Thae Chaung is about 900 km (560 miles) northwest of Dawei and holds internally displaced people, most of whom are stateless Rohingya.
“They said they ran away from the camp. They said they intended to go to Malaysia,” said Moe Zaw Latt, adding authorities were preparing to send them back to Sittwe on Tuesday.
Photographs in media showed police standing by as passengers - many of them women in headscarves and children - huddled on the deck.
The boat resembled vessels the Rohingya typically use to escape the apartheid-like conditions in Rakhine State, where their movements and access to services are severely curtailed.