A Malaysian tanker has exploded as it was being loaded with methanol leaving one crew member dead and four missing, police said, blaming a bolt of lightning.

The accident happened at a methanol terminal run by national energy firm Petronas on the South China Sea island of Labuan, off Borneo, said the ship's operating company MISC.

Three loud blasts rocked the island today and the 38,000-tonne Bunga Alpinia was left about "80 per cent destroyed", Labuan police chief Saiman Kasran said.

"There was heavy rain and lightning at that time," he said.

"We presume the fire was caused by a lightning strike. We found one body and four crew members are missing."

MISC, which is a subsidiary of Petronas, said in a statement the chemical and palm oil tanker had 29 people on board - 23 Malaysians and six Filipinos - and 24 were brought ashore safely.

It gave no further details.

AFP