The accident occurred at a methanol terminal run by national energy firm Petronas on the island of Labuan off the Malaysian portion of Borneo island, the shipping company MISC said.
The tanker was believed to be carrying liquefied natural gas (LNG) at the time. MISC said in a statement that the 29 crew members comprised Malaysians and Filipinos.
24 crew members have been safely brought to shore and five still unaccounted for, the statement said.
Firemen who rushed to the scene were forced to withdraw when a series of explosions occurred, Star online said.