At least 21 bodies have been found since the vessel went down on Thursday - 12 in Malaysia and nine in neighbouring Thailand - the regional head of Malaysia's maritime agency, Romli Mustafa, told reporters.
Without life jackets, it might be difficult for many to survive even 24 hours, but some could be holding on to floating objects and search operations would continue, he added.
"Weather conditions are not so friendly but anyhow, we're trying our level best," Romli said.Â
So far, 13 survivors had been rescued, he added.
Long persecuted in Buddhist-majority Myanmar, the mainly Muslim Rohingya face escalating violence in their war-torn homeland and worsening conditions in crowded refugee camps in neighbouring Bangladesh where 1.3 million of them live.
Hundreds of Rohingya people boarded a vessel bound for Malaysia two weeks ago, and were transferred onto two boats on Thursday, according to Khairul Azhar Nuruddin, police chief on Malaysia's northern Langkawi island.
The smaller ship carrying around 70 people sank near Langkawi the same day and the fate of the other boat carrying 230 passengers remains unclear, Malaysian authorities said.
Among those who took a boat to Malaysia two weeks ago was 29-year-old Mohammed Ibrahim, according to his elder brother, Mohammed Younus.
"He left for Malaysia without telling anyone," he told Reuters from the refugee camps in Bangladesh.
"If I had known, I would never have let him go. He has a wife, three children - a three-year-old son and 10-month-old twin girls. Who will take care of them?"
In the last week of October, multiple boats carrying Rohingya left Cox's Bazar in Bangladesh, said Chris Lewa, director of the non-profit Arakan Project, which tracks the voyages.
It typically takes a week to 10 days to reach Malaysian waters, Lewa told Reuters. The boats might also have stopped in waters off Myanmar to pick up Rohingya coming from inland areas of Rakhine state, where a civil war has made displacement worse, she added.
More than 5100 Rohingya boarded boats to leave Myanmar and Bangladesh between January and early November this year, and nearly 600 of them have been reported dead or missing, according to data from the UN Refugee Agency.
Muslim-majority Malaysia has long been a favoured destination for Rohingya fleeing persecution, although the country does not recognise refugee status.
Malaysian police said those rescued had been detained pending an investigation into potential immigration offences.
Thailand and Malaysia have deployed air and sea patrols in a search operation that could last a week, Malaysian maritime official Romli said.
Information received by the agency indicated that the first boat the Rohingya boarded had left from Rakhine state, which borders Cox's Bazar in Bangladesh where the sprawling refugee camps are located, Romli added.
