According to witnesses, passengers ran screaming from the boat after the blast at 1pm local time (6pm GMT).
The ferry had reportedly just arrived at the dock only minutes before it happened.
The cause of the blast is unclear at this stage, but early reports suggest it was a gas explosion.
Authorities in Quintana Roo are investigating the shocking incident.
Rodrigo Apolimar, a firefighter, said a number of people are injured.
He also revealed there were tourists on board.