The submarines are to have their equipment upgraded
Seven Trafalgar-class attack submarines, which are stationed at Devonport Dockyard in Plymouth, are due to have their command, tactical weapons and sonar systems upgraded as part of a rolling programme.
But a government report from the National Audit Office said some suppliers have "experienced major difficulties and continue to struggle to meet the required programme".
Delays have also been caused by software engineering problems in the sonar system development programme.
A Ministry of Defence (MoD) spokeswoman said the setbacks were caused by delays in the general upkeep programmes for each submarine.
However, the spokeswoman also said that these were not related to last year's problems when the fleet was recalled amid reactor safety fears.
Four of the Trafalgar submarines were found to have faults in their reactor cooling systems and had to be recalled and repaired.
The fault stranded HMS Tireless in Gibraltar for over a year before it could be made seaworthy again.
The submarine's year-long presence at the UK base on the Rock strained relations with Spain when thousands of environmentalists protested in both Spain and Gibraltar against the submarine being moored there.
'Minimal impact'
The crew of Tireless also said it was unsatisfactory because they were only able to train on simulators.
The reactor coolant leak has since been fixed.
The spokeswoman said the software development problems had "minimal operational impact on the submarines".
So far, only one Trafalgar-class submarine, HMS Torbay, has had the equipment installed during a recent three-year refit by Devonport Management Ltd (DML), the company that runs the dockyard.
A DML spokesman said its role in the tactical weapons system upgrade was to install various items of equipment.
He said: "Any delays to this programme are not connected with DML's refitting role."
The report from the National Audit Office is part of an annual check on major military contracts.
Since 1998, the Ministry of Defence has been working under new processes known as Smart Acquisition, to enable the Department to buy military equipment "cheaper, faster and better".
Sir John Bourn, head of the National Audit Office, said: "I welcome the signs that the Ministry of Defence is beginning to bring delays on major projects under control, and is continuing to control costs on major projects.
But he added: "I am concerned, there are no measures to fully assess whether all of the benefits of Smart Acquisition are being achieved.
"The MoD should give priority to establishing such indicators."