A Flydubai spokesperson confirmed the flight "experienced an incident while en route", and that updates will be issued as further details become available. "Our teams are working closely with the relevant authorities," it added.
Data from Flightrader24 shows a rapid descent for the plane over Saudi Arabia, just two hours after take-off, descending more than 17,000 feet (over 5,000m) in less than two minutes just after 05:21 UTC (06:21 BST).
At 05:40, the flight briefly entered Jordanian airspace before looping back into Saudi Arabia minutes later, where it then began its descent for landing.
The Israeli air force dispatched fighter jets in response to the incident and Prime Minister Benjamin Netanyahu held urgent consultations on the incident.
In a statement, Netanyahu said the situation is under control and that efforts are under way to return the Israeli passengers home from Saudi Arabia.