The £3.2bn carrier suffered a saltwater pipe breach in March.
It meant thousands of gallons of water poured into the flagship, The Sun reported.
A Royal Navy spokesman said: ‘There was a minor breach of a saltwater pipe in March which was fixed swiftly and had no impact on the ship's programme.’
The leak comes after she suffered with a leaky propeller in 2017, and saw neck-high flooding in July 2019.
Her sister ship is still in port in Portsmouth after suffering a leak in October causing £3.3m of damage to the ship.
Portsmouth South MP Stephen Morgan, Labour’s shadow armed forces minister, told The Sun: ‘Repeated floods raise questions about the capability of our carriers. HMS Queen Elizabeth will perform work vital to our national security.
‘The government must be upfront about readiness.’