Charles was scheduled to visit HMS Queen Elizabeth on the last day of her tour of Egypt, but hours before the event his Clarence House office announced that the visit would not take place.
The pilot at the controls of an F35, estimated to be worth around £ 100million, ejected from the plane before crashing into the ocean on Wednesday and was subsequently rescued.
Former Private Tobias Ellwood, who chairs the Commons Defense Select Committee, said he had “a lot of questions” about the crash.
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A spokesperson for Clarence House said: “For operational reasons the visit of HMS Queen Elizabeth has been canceled. “
During the visit Charles was scheduled to meet Commodore Steve Moorhouse, Commander of the Carrier Strike Group, and Captain Ian Feasey, Commander of HMS Queen Elizabeth.
He was also scheduled to witness the launch of an F35 jet from the flight deck before meeting some of the ship’s crew, including the US Navy and Marines.
The ship’s jets have previously participated in strikes against the remnants of the so-called Islamic State in Iraq and Syria.
The 65,000-ton Royal Navy flagship returns to the UK after its inaugural mission, which included exercises with the Indian Army.
It was part of the Carrier Strike Group deployment to the Indo-Pacific amid heightened tensions with China in the region.
The jets are operated by the famous 617 Squadron, also known as the “Dambusters” Squadron.