More than 100 migrants aboard the cargo ship are said to have acted after being told they would be taken back to Libya, BBC reports.
Malta's military said the ship would not be allowed into its waters. Italy's Deputy Prime Minister Matteo Salvini described the hijackers as "pirates".
This comes as the EU says it is ending navy patrols in the Mediterranean.
The Elhiblu cargo ship is believed to be carrying more than 100 migrants. Its present location is unclear, as are the circumstances of the rescue off Libya.