Two nuclear submarine crew members are being investigated for disobedience after leaving the vessel amid fears about its safety, the government said.
HMS Trafalgar has undergone 15 months of repairs
But reports the ship, HMS Trafalgar, was in an unfit state and that some of the crew had "mutinied" were rejected by junior defence minister Lord Bach.
Eleven crew were allowed ashore last week after expressing safety fears.
Trafalgar had been due to begin operational tests following minor repairs at the Faslane nuclear base.
But before it sailed, 12 crew members expressed fears about their safety onboard.
Of these, one stayed on board while the remaining 11 left the vessel and were medically examined.
The submarine's commanding officer had believed that most of the crew members concerned might be suffering from some sort of stress and wanted them to be properly examined by doctors, Lord Bach said.
Five were now back on board and the remaining four had been medically downgraded for a month.
The pair involved in the probe were being investigated for disobedience to orders and not for mutiny, he said.
Trafalgar had been out of service since it ran aground off the Isle of Skye in 2002 during a training mission.
Speaking in the Lords at question time, Lord Bach said it had since completed a major repair at Devonport in Devon.
"Rigorous tests were undertaken to validate all aspects of her seaworthiness, before sailing," he said.
"Recent press reports alleging that the vessel was in an unfit condition to
proceed to sea were completely unfounded," he added.
And he denied that any of the 11 crew who left the submarine were safety experts.
Lord Bach refused to confirm claims by Liberal Democrat peer Lord Methuen that the sub had sailed with more than 250 defects, including unacceptably high radiation levels in its reactor compartment.
But it was "not unexpected" for there to be minor defects following a maintenance period, he said.
The Ministry of Defence confirmed last week that there had been some faults but not enough to stop the Trafalgar going to sea.
And it denied there was any radiation leak.
Three sailors were injured when the Trafalgar ran aground in November 2002 and an estimated £5m of damage was caused to the vessel.
In March, a court martial hearing reprimanded Commander Robert Fancy and Commander Ian McGhie, both 39, for their part in causing the vessel to ground in 2002; both pleaded guilty to negligence.