The explosion occurred when a fire broke out on board the Malaysian International Shipping Corporation-owned Bunga Alpinia 3 alongside the Petronas Methanol terminal in Labuan.
The Malaysian Maritime Enforcement Agency (MMEA) said the body of the dead crewman identified as 28-year-old Shahril Azmi Baharuddin, was found floating in the sea this morning.
MISC said in a statement that the 29 crew members comprised Malaysians and Filipinos.
Twenty four were safely brought to shore, the statement said.
MMEA coordinating officer Lt Comm Azmi Mohd Dahan said three people sustained minor burn injuries.
Firemen, who rushed to the scene, were forced to withdraw when a series of explosions occurred.