An Airports Authority spokeswoman said Continental Airlines' Flight 90 was intercepted after it failed to identify itself upon entering Israeli airspace.
Following anti-terror procedures, two Israel Air Force jets intercepted the plane and guided it back over the Mediterranean Sea until communications were restored.
The plane, a Boeing 777, was on a scheduled flight from Newark, New Jersey in the United States. All passengers and crew disembarked safely, Israeli officials said.
The Transportation Ministry said it was investigating whether there was a technical reason for the initial lack of communication between the plane and Israeli ground control.
An Israel Air Force official said that due to the sensitivity of the incident, the prime minister and defense minister were also informed on details of the matter.
"From the moment that we lost contact with (the jet) we treated the incident as a possible terror act. When the fighter jets approached the plane, they guided it west. It contacted us and that's how we were sure it was not a terror attempt," said the source.
Hanan Greenberg contributed to the report