Indian national Sunil James and two crew have spent more than a month in detention, the Times of India reported.
He had called in Lome to report the attack on the 32,000-dwt Ocean Centurion (built 1999), but instead found himself arrested by local authorities.
Indian diplomats are now in touch with Togo to resolve the issue.
James was injured in the attack and received stitches to his wrist.
His wife Aditi told the newspaper: "My husband Sunil James got off the ship on 30th July for investigation and for a day he was put up at navy barracks. On 31st evening he was taken into custody along with two others for investigation.
"The lock-up in which he is put is suitable for 20 inmates; however, 80 are kept in it. He has no food, water, sleep or any basic amenities and is in a cell with criminals.''
It is reported that charges are to be brought against the men, who have complained they have been forced to sign documents without understanding their contents.
The vessel is operated by Union Maritime. It is currently underway off Lome, according to AIS data.
