Police in Cox's Bazar in Southeastern Bangladesh said the 13 fishermen were found in the ice chamber of their boat, which was found anchored at the port.
"We still don't know what really happened, but the boat was brought from the Bay of Bengal and anchored at the terminal by unidentified people," one policeman said, adding that the pirates fled with the boat's engine along with other booty.
Local residents saw the unmanned boat and informed the police.
"Following the search, 14 fishermen were found in the ice chamber with 13 already dead," he said. The sole survivor was rushed to a local hospital.
The boat went to the high seas on October 25. No other details were immediately available.