The tanker, Elhibru 1, is now heading to a Maltese port with the crew and migrants, who will be handed over to police.
More than 100 migrants who had been rescued by the ship hijacked it after being told they would return to Libya.
They had ordered the ship's captain to head north towards Europe.
In a statement, the Armed Forces of Malta (AFM) said they had established communications with the captain of the ship when it was still proceeding towards Malta.
The captain said he was not in control of the vessel and that he and his crew were being forced and threatened by a number of migrants to proceed to Malta.
A patrol vessel stopped the tanker from entering Maltese territorial waters, and a special operations unit team was dispatched to board and secure the vessel, the AFM said in a statement.
Italy's interior minister, Matteo Salvini, had earlier called the migrants "pirates" and said they would not be allowed to dock in Italy.
He described the act as "the first piracy on the high seas with migrants", according to the Associated Press news agency.
The incident comes as the EU says it is ending navy patrols in the Mediterranean.
The EU says the decision to suspend Operation Sophia in September follows a request by Italy.
The mission was put in place four years ago to deter people smugglers and rescue migrants trying to reach Europe by boat. Tens of thousands have been saved.
Lately, the mission has largely targeted smuggling networks as the number of people making the crossing dropped sharply following a controversial deal between the EU and Libya.
But Mr Salvini, the leader of the right-wing League party, has blamed Operation Sophia for continuing to bring rescued migrants to Italian shores.
He has been at the centre of a number of international row over his refusal to allow migrant ships dock in Italian ports.
