The £3 billion warship left Portsmouth Naval Base last Saturday on its way to the US for diplomatic visits and exercises, including flight trials with the F-35B Lightning jets.
The Navy announced on Friday that sister ship HMS Queen Elizabeth, the fleet flagship, would sail next week to take over its US duties.
Shortly after the Prince of Wales, the Nato flagship, sailed last Saturday, a mechanical fault was discovered with the starboard shaft.
The departure of the 65,000-tonne ship had already been delayed from the previous day because of a technical problem but a decision was taken to sail anyway.
The carrier sailed back slowly to Stokes Bay at Gosport, Hampshire, on Monday travelling at a rate of four knots accompanied by tugs for the return journey to calmer waters.
Navy divers have been inspecting the ship and found that a coupling on the starboard propeller shaft had failed.
The shaft is a combination of steel poles joined together with a shaft coupling, one of which has failed.
It is understood this was caused by a mechanical failure not because of a failure to keep the coupling greased.
HMS Prince of Wales left Stokes Bay on Saturday afternoon accompanied by three tugs and returned to Portsmouth Naval Base under the power of a single propeller.
A wake could only be seen on the port side of the ship as it returned while being assisted by the tug Apex and two pilot boats.
Shoppers and well-wishers lined the harbour walls to catch a glimpse of the giant ship’s return, dwarfing the buildings of Old Portsmouth as it passed by.
It will now unload crew and equipment and remain at the port while further inspections are carried out before it heads to dry dock for repairs, probably at Rosyth in Scotland where it was built.
The Nato flagship had been sailing to undertake training exercises with the US Navy, the Royal Canadian Navy and the US Marine Corps.
Now this is an extremely unusual fault and we continue to pursue all repair options
The crew of the HMS Queen Elizabeth have been notified they will now be sailing to the US, altering its previous plans for deployments to the Baltic and Mediterranean this autumn.
Navy chiefs and the Government are believed to be assessing which of the US commitments including the Atlantic Future Forum in New York at the end of September are essential for a carrier and which can be carried out by other ships from the fleet.
The Navy had said prior to the departure of HMS Prince of Wales that notable port stops during the three-month deployment would be in New York, Halifax in Canada and the Caribbean.
Rear Admiral Steve Moorhouse, director of Force Generation, who is responsible for making sure Royal Navy ships are ready to deploy, confirmed on Friday that HMS Queen Elizabeth would take over the US duties.
He said: “Royal Navy divers have inspected the starboard shaft of the shift and the adjacent areas and they have confirmed there is significant damage to the shaft on the propeller and some superficial damage to the rudder but no damage to the rest of the ship.
“Our initial assessment has shown that coupling that joins the final two sections of the shaft has failed.
“Now this is an extremely unusual fault and we continue to pursue all repair options.”