The Malaysian Maritime Enforcement Agency (MMEA) warned that the gunmen have become cleverer and more cautious in recent months.
They are picking targets more carefully due to increased patrols from authorities, the Star daily reported.
The MMEA said the tactic first came to light at the end of last year when eight men were caught in waters off Pengerang.
MMEA southern region enforcement chief Adon Shalan said gangs were using ferry boats and water taxis to ply the route between Batam and Malaysia or Singapore.
"Once these scouts find a worthwhile or easy target, another pirate vessel disguised as a sea trader will approach the marked vessel, offering to sell fruits, food or goods to the crew," he added.
"While the crew are buying the items, the pirates are counting heads and checking out security measures on the targeted vessel before attacking."
Some of the pirates would even befriend the crewmen to try to find out what kind of cargo they were ferrying, he added.
Shalan added: "Unlike in the movies, the pirates do not hoist a black flag with a skull and crossbones insignia, or wear tattered clothes."
