Eight suspects were arrested on Friday for attacking the 7,301-dwt Orkim Harmony (built 2009).
A senior executive of the Malaysian Maritime Enforcement Agency (MMEA) said five more men used a tug to approach the ship, the Straits of Malacca reports.
Indonesian authorities found the tug while conducting search operations in the area.
The MMEA executive also said the suspects detained were not amateurs but seasoned criminals who “knew what they were doing”.
The Magna Meridian-owned ship was reportedly carrying 5,879 tonnes of RON95 fuel worth MYR 21m ($5.5m) which belongs to state-owned oil company Petronas.
It lost communication with its owners on 11 June and was the second vessel under the umbrella of Orkim Ship Management to become a target at that time.