The Sunday Times newspaper said the ship named as MV Boreal was boarded by customs sleuths under military escort.
The report said the ship's agent had submitted documents to clear wheat imported from the Canadian Wheat Board, before the vessel arrived in Trincomalee and two days before a budget proposed a new import tax on wheat.
The ship is carrying a cargo valued at 3.2 billion rupees, The Sunday Times said.
The report said customs were probing a part of the cargo consisting of 9,000 tonnes of wheat, which was originally due for Singapore.
Prima Ltd has issued a certificate that the consignment was being supplied free of charge by Prima Ltd in Singapore to Prima Ceylon Ltd under an agreement for transshipment services.