The ministry said the jet’s British pilot ejected safely from the Wednesday morning (Wednesday evening AEDT) crash and returned to the HMS Queen Elizabeth.
An official investigation was opened. The ministry declined to provide further details.
The F35s, estimated to be worth about £100 million ($185.5 million) each, are on board the £3 billion ($5.6 billion) HMS Queen Elizabeth.
Jets from the vessel previously participated in strikes against remnants of the Islamic State group in Iraq and Syria.
The aircraft carrier has been on its first operational deployment over the past six months, carrying out visits to 40 countries including India, Japan, South Korea and Singapore.