The British F35 jet of the British flagship aircraft carrier crashed into the Mediterranean during the flight, and the pilot crashed in the first such situation that hit HMS Queen Elizabeth.
No hostile activity is believed to be involved.
Research is likely to focus on possible technical or human errors.
A Defense Department spokesman said: “HMS Queen Elizabeth’s British F35 pilot crashed during a routine flight in the Mediterranean this morning.
“The pilot has been safely returned to the ship and the investigation has begun, so it would be inappropriate to comment further at this point.”
The £ 100 million next-generation RAF F35 jet is believed to be at sea and has not yet been found.
The rack features eight British F35 jets as well as 10 American F35 jets. They are a B version of the Lockheed Martin jet that can take off a short distance and land on a scaffold.
HMS Queen Elizabeth returns to the UK for more than seven months at sea after spending a maiden voyage to the Far East and back.
The incident occurred at around 10 a.m. British time in international waters. No other ships or aircraft were involved.
A comprehensive military air investigation is being carried out as a matter of urgency.
All other F35 operational and training flights will continue.