In a message to Israel's foreign minister, El Al Airlines CEO Eliezer Shkedi said that flights are nearly empty, and the airline cannot afford the high security and operating costs.
El Al declined comment. But Irena Etinger, spokeswoman for Foreign Minister Avigdor Lieberman, confirmed the letter.
Under their historic 1979 peace accord, Israel and Egypt agreed to operate flights between the countries.
But few Israelis felt safe visiting Cairo, and their numbers have dwindled following last year's Egyptian revolution.
The letter did not say when El Al would halt flights. Any such move would be mostly symbolic as the airline has only provided flights sporadically since the Arab uprising erupted last year across the Middle East.
Foreign Ministry spokesman Yigal Palmor said if El Al cancels its service, another airline must provide Cairo flights.