The affected flights include ones to and from New York, Washington, Philadelphia and Boston.
Several flights at airports in Ottawa, Montreal and Halifax were also cancelled due to Irene, which hit the US East Coast on Saturday. Irene has been downgraded from the hurricane to a tropical storm and may later be further downgraded to a post-tropical storm.
"I want people to understand that this is not over," US President Barack Obama said on Sunday evening from Washington. "The recovery effort will last for weeks or longer."
Millions of homes and businesses have been blacked out and at least 20 people died as Irene pounded through the US states of North Carolina, Virginia, Maryland, Delaware and Pennsylvania, as well as New York City and Washington, DC.