The incident took place on Thursday 1.5 nautical miles off Sandakan, in the northeast part of the country.
IMB said two robbers made their way on to the vessel using the anchor chain.
The crew raised the alarm in time and the thieves abandoned the stolen items and escaped.
No injuries have been reported, while the name of the vessel has not yet become known.
A total of 24 armed robberies were reported in Asia in August.
The government is establishing a task force to combat piracy gangs after increased pirate activity has been noticed in the Malacca and Singapore Straits.
