Rescuers were combing an area of 170 square nautical miles near Langkawi island on Saturday after a boat with 300 people on board left Myanmar's Rakhine state three days earlier, regional maritime agency head Romli Mustafa said.
Images from the agency showed one survivor covered with a sheet and another on a stretcher.
Myanmar's impoverished Rakhine state has suffered years of conflict, hunger and ethnic violence mostly targeting the Rohingya Muslim minority community.
Driven out of Rakhine state following a brutal 2017 military crackdown, about 1.3 million Rohingya live as refugees in densely-packed camps in neighbouring Bangladesh.
Malaysian state media Bernama cited Kedah province police chief Adzli Abu Shah as saying people initially boarded a large vessel from Myanmar but were instructed to transfer onto three smaller boats, each carrying about 100 people, to avoid detection as they neared Malaysia.
The status of the other two boats was unknown and a search-and-rescue operation was ongoing, he said.
Facing violence at home in Myanmar and increasingly difficult living conditions in Bangladesh, Rohingya from both countries regularly attempt perilous journeys by sea, including to Malaysia.
More than 5100 Rohingya have taken boats to leave Myanmar and Bangladesh between January and early November this year, with nearly 600 people reported dead or missing, according to data from the UN Refugee Agency.
