Andy Coles, 47, lost his command of the submarine yesterday, but he will continue to serve in the Royal Navy. A final decision on whether he will face a court martial has yet to be made.
A Royal Navy spokesman said: “From yesterday, November 26, he was removed from command of HMS Astute.
“He’s going to continue with the Royal Navy. He will be reappointed to another post.
“It’s an internal administrative matter between Commander Coles and his senior officers.”
It is not known what Commander Coles’ new post will be, and the spokesman said a new commanding officer of HMS Astute will be appointed in the near future.
HMS Astute ran aground on 22 October and was eventually freed when the tide began to rise.
The nuclear submarine was then damaged in a collision with the coastguard tug the Anglian Prince. It returned to the Faslane base three days later.
The Navy spokesman said the final cost for repairs are still being calculated, with unconfirmed reports suggesting the bill could run into millions. The repairs are now complete and the spokesman said it would be “paid out of the existing MoD budget”.