A leak which forced the HMS Queen Elizabeth aircraft carrier to return to port saw water rise "neck-high" in flooded areas, the BBC has been told.
The biggest and most powerful warship ever built in Britain experienced the leak during sea trials on Tuesday.
It was believed to have come from a ruptured pipe which caused some internal damage, the BBC learned.
The Royal Navy described it as a "minor issue relating to water from an internal system" on the £3.1bn ship.
On Wednesday a Royal Navy statement said the ship had returned early from sea trials as a "precautionary measure" with an investigation into the cause underway.
It said: "At no point was there damage or breach to the hull. The issue was isolated as soon as possible and all water has now been pumped out. "
The BBC's defence correspondent Jonathan Beale said the leak was "more serious than most".
He added: "A source told the BBC that in some compartments the water was neck high."
The BBC has contacted the navy for further details.
The Royal Navy's future flagship had been due to return to Portsmouth for planned maintenance.
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The 900ft (280m) long warship left Portsmouth Naval Base last month for five weeks of sea trials and training.
The ship has suffered a number of other issues including a shaft seal leak, which caused the ship to take on 200 litres of water every hour, and the accidental triggering of the sprinklers in the hangar.
In May the captain of the aircraft carrier was removed from the ship amid claims he misused an MoD car.