The department urged residents in the West Kowloon area to close their doors and windows because of the acrid smoke from the blaze.
The barge, which is carrying scrap metal, caught fire late on Wednesday afternoon and was upgraded to a number 3 alarm just after 11 pm.
Firefighters with breathing apparatus and two fire boats were dispatched to the scene, though this was later reduced to a single fire boat.
The fire was largely put out by 8.20am on Thursday and no casualties were reported.
Some district councillors said residents around Mei Foo and Cheung Sha Wan complained of feeling unwell.
Last updated: 2021-06-03 HKT 09:00