The radar equipment had been seized by customs officials shortly after the consignment arrived last month from Australia, en route to the Netherlands, as it did not have the necessary permit.
The Star quoted Nusajaya district police chief ACP Nor Hashim Mohamad as confirming that a police report had been made.
The report also quoted Customs Department assistant director-general (enforcement) Paddy Abd Halim as saying an internal investigation had started into how the equipment, not easy to move, could go missing.
The equipment was in a container.
All military equipment being shipped out of, or in transit at any Malaysian port, requires a special permit from the international trade and industry ministry (Miti), according to the report.
No such permit or other supporting documents were produced when requested by port and customs officials.
The Star reported that the authorities were also looking at the possibility that the consignment could have been loaded onto another vessel and shipped off to the Netherlands discreetly to avoid further problems.
The report quoted sources as saying such sensitive equipment required a permit under the Strategic Trade Act 2010 from Miti.
The Act is aimed at preventing sensitive items from falling into the hands of extremists, who may use these for nuclear armament and weapons of mass destruction.
Fines for breaching the law can be as high as RM10 million and those convicted can face even the death penalty.