Defence Minister Juwono Sudarsono said the IMB in its recent report had deliberately attempted to undermine the South-east Asian nation's competitiveness on the world stage.
Mr Sudarsono said that the report also implied that the nation's security forces were incapable of maintaining law and order in the Malacca Strait, through which half of the world's oil shipments travel.
'I am afraid that those numbers (are intended) to weaken our competitiveness. It was written as if our armed forces and police are incapable of maintaining order (in the strait),' Mr Sudarsono told ElShinta radio.
'(Piracy cases) decreased a lot last year,' he said.
London-based IMB reported last month that Indonesian waters accounted for nearly a quarter of all pirate attacks in the first three months of the year.
The international maritime watchdog said attacks were declining in the area, but seafarers should remain on alert while sailing there.
It also said that the vast archipelago nation should be applauded for its efforts to reduce the number of attacks.
The three littoral states bordering the strait - Singapore, Malaysia and Indonesia - have implemented several security measures, including coordinated air and sea patrols, to secure the vital waterway.
Mr Sudarsono's comments came one day after the Indonesian navy said it needed a larger and better equipped fleet to prevent a possible terrorist attack in its waters.
'Currently we have around 135 warships and it is not on par with our vast national marine area that needs to be secured,' navy chief of staff Slamet Subijanto said, quoted by state agency Antara.