HMS Astute was on sea trials when it became stuck near Skye on October 22, 2010 and ended up marooned for several hours.
Its commander Andy Coles, 47, was later removed from command of the vessel.
A service inquiry into the grounding, published today, found there were a variety of causes for the incident.
The report said: ''The root causes of the grounding were non-adherence to correct procedures for the planning and execution of the navigation combined with a significant lack of appreciation by the Officer of the Watch (OOW) of the proximity of danger.
''However, a number of additional causal factors were present, including some deficiencies with equipment.''
Rear Admiral Ian Corder, head of the Submarine Service, said that the organisation had learnt from the incident.
HMS Astute was on sea trials when it became stuck on a shingle bank on the west coast of Scotland on October 22.
The vessel ran aground off the coast of the Isle of Skye but it was freed by the evening of the same day when the tide began to rise.
But it was later damaged after a collision with the Coastguard tug the Anglian Prince, which was sent to free it.
It is believed a crew transfer from the shore to the submarine was being carried out when the incident happened between the Isle of Skye and the mainland.
In June 2007 the mammoth nuclear-powered HMS Astute was named and launched by the Duchess of Cornwall.
A contract worth £3.5 billion was signed for the first three boats in the Astute class but there is no specific figure per submarine.
In August last year, HMS Astute was welcomed into the Royal Navy during a commissioning ceremony at Faslane Naval Base on the Clyde.
The submarine weighs 7,800 tonnes, equivalent to nearly 1,000 double-decker buses, and is almost 100 metres (328ft) long.
Its Spearfish torpedoes and Tomahawk cruise missiles are capable of delivering pinpoint strikes from 2,000km (1,240 miles) with conventional weapons.
The submarine's nuclear reactor means that it will not need refuelling once in its entire 25-year life and it makes its own air and water, enabling it to circumnavigate the globe without needing to surface.
Built by defence giant BAE Systems at Barrow in Furness, Cumbria, it is the first in a fleet of six which will replace the Trafalgar class submarine.
As the base port of all the Navy's submarines from 2016, Faslane will be home to the whole Astute class.
The accident happened almost exactly 50 years after the UK's first nuclear submarine was launched. HMS Dreadnought was launched on October 21 1960 by the Queen.
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