Thick black smoke earlier rose over the hotel and flames could be seen on the ground and first floors, a witness said.
The fire was apparently caused by an electrical short-circuit, Kamran Lashari, Islamabad's top administrator, told the Reuters news agency.
Al Jazeera's Imran Khan, in Islamabad, said that contradictory reports were emerging about where the fire started, with some saying it was the basement while others said it originated in the kitchen.
The hotel has taken protective measures to prevent further attacks after the bombing, but these served to hamper efforts by the fire service to extinguish the blaze, Khan said.
The Marriott reopened in late December, just over three months after the September 20 bomb attack blamed on Islamist fighters.
The blast sparked a fire that gutted the building, one of two top hotels in the capital and long a favourite haunt of diplomats and wealthy Pakistanis.