Blair told radio station Newstalk 1010 the officer was "shameful" to pretend he was one of the 1,400 riders on the GO train when it became trapped by flood waters during the evening rush hour.
CBC said the officer was Const. Nickolas Dorazio. The network said he was working to help rescue the passengers, but told their TV crew he was stuck on the stranded train and even draped an orange towel around his shoulders for effect.
Blair says the force has disciplined the officer for his "stupid behaviour" that Monday night.
The police chief says the officer's conduct was an "eyebrow raiser" that undermined public confidence in the force.
Police and firefighters used small inflatable boats to ferry the trapped passengers a short distance to higher ground, with the evacuation taking some seven hours.
"We've dealt with this. The matter's been looked into," Blair said, without going into detail.
"It was somebody's idea of a joke, and it was not funny."
Toronto Police Association president Mike McCormack said the officer regrets what happened and will face the consequences for his actions, which may see his pay docked.
"There was no malice meant by it. It was just misplaced humour that went too far."
Record-smashing rains that night knocked out power for hundreds of thousands of residents across the Greater Toronto Area, including the majority of Mississauga, and so badly flooded some roads and major highways that drivers abandoned their vehicles.
On board the ill-fated Richmond Hill line GO train, murky brown water spilled through the bottom floor of the carriages and sent riders fleeing for dry ground in the upper sections of the train.
The transit service later gave a $100 credit to passengers stuck on the train.
Also on HuffPost