Defence Minister Bill Blair says a Royal Canadian Air Force plane has left Tel Aviv with 130 people on board.
The departures board at the airport shows that flight CFC 4169 left for Athens this afternoon local time.
The federal government said Wednesday that flights could begin leaving as early as today, with up to 150 passengers on board.
Officials say around 700 Canadians in Israel have asked for help to leave the country since violence broke out on Saturday.
Canada does not usually provide military air transportation when commercial flights are still operating, but the government says people have been asking for help because it's difficult to get tickets.
A second Royal Canadian Air Force flight is listed on the departures board for this evening, and a third for Friday afternoon.