Defense Minister Bill Blair said a Royal Canadian Air Force (RCAF) plane left Tel Aviv with 130 people on board.
The airport departure board shows that flight CFC 4169 departed for Athens on Thursday afternoon local time.
The federal government said Wednesday that flights could begin taking off as early as Thursday, with up to 150 passengers on board.
Authorities say about 700 Canadians in Israel have requested help to leave the country since violence erupted on Saturday.
Canada generally does not offer military air travel when commercial flights are still operational, but the government says people have asked for help because it is difficult to obtain tickets.
A second ARC flight is scheduled for Thursday evening, and a third for Friday afternoon.
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