"They were found near Tho Chu Island at about 6.30am. They were on a life raft and claimed they were from a fishing boat that sank," Royal Navy Malaysian chief Abdul Aziz Jaafar said.
Aziz said his men were confirming if those arrested were the hijackers of MT Orkim Harmony oil tanker.
"We are checking their story and investigation is still going on," he was quoted as saying by The Star online.
Aziz said the crew members are safe except for an Indonesian seamen who was shot in the thigh; he was being treated.
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The Navy chief said the oil tanker is sailing back to the northern Kuantan port, escorted by a navy ship and is expected to arrive at the port tomorrow.
He said three navy ships and two helicopters were deployed to locate the pirates, who were armed with pistols and machetes, and spoke with Indonesian accents.
The crew comprised 16 Malaysians, five Indonesians and a Myanmar national.
It was scheduled to arrive at the Kuantan Port at 10.30 AM the following day.
Authorities said that MT Orkim Harmony had been repainted and renamed 'Kim Harmon' by the pirates. Aziz has also tweeted pictures of the tanker.
It was the second tanker hijack case this month. Another Malaysian tanker carrying diesel was hijacked on June 4 in the same area and was released after the fuel was siphoned off by the pirates.
Southeast Asia alone witnessed 38 pirate attacks during January-March.