HMS Astute became stuck during sea trials on Friday, in a channel between the Isle of Skye and the mainland.
The Navy’s highest-tech submarine is understood to have strayed several hundred yards outside the safe sea lane marked on Admiralty charts.
After being stuck on a shingle bank for 10 hours, the £1.6billion vessel was eventually towed free by a tug boat.
The Ministry of Defence (MoD) said it was not a “nuclear incident” and pledged a “full and thorough” investigation.
It will consider if any crew were negligent, and the submarine’s skipper, Commander Andy Coles, could face the prospect of a court martial.
Yesterday, it emerged he had described himself as getting too old for the job in an interview conducted in the summer.
He said: “When I leave her next May, I probably won’t go to sea on a submarine again.
“I’m 47 now and it’s time for someone younger.”
Coles admitted having “close shaves” in the vessel – which can be witnessed by crew members on high-definition television screens.
He said: “In the old days, you could spin around, see you’d had a close shave and think to yourself, ‘I’ve got away with it’. Now everybody knows.”
The skipper also told how he had previously ignored advice not to sail HMS Astute in bad weather. Coles sailed Astute from the Burrow-in-Furness yard, where it was built, into a violent storm last November.
He added: “We left in the teeth of a force eight gale, with the rain lashing in.
“We were advised not to sail, but we still went and I’m glad we did. If ever we needed a test, going out into that was it.”
Astute was moored in deep water on Saturday while its hull and rudder were checked for damage.
Yesterday, the 100-yard vessel began to return to Faslane on the Clyde above water and under its own power, escorted by a tug and a Royal Navy minehunter.
A spokesman for the MoD said it would be “inappropriate” to comment on the possibility of disciplinary action until the investigation is complete.
Kyle lifeboat operations manager Ross McKerlich saw the incident and said: “If he had gone another 200 yards, he would have hit a big rock which would have split its back, and who knows what would have happened then."