“We are dealing with a potential explosive device,” Toronto police said in a tweet.
Two residential buildings near the ferry terminal also were evacuated and a third partially evacuated.
The airport said its runway was closed and two Air Canada flights were diverted to Hamilton, Ontario.
Passengers stranded inside the terminal for several hours said they were being evacuated by water taxis.
“Runway is closed for the evening. Porter has completed its flight schedule for the evening. Two Air Canada flights diverted to Hamilton. Passengers remaining in terminal being evacuated at present. Tunnel/ferry remains closed,” Billy Bishop Airport said in a tweet.