Disposal of the retired submarines involves a series of inter-related tasks to remove the fuel, take out radioactive parts and recycle the submarine.
Since 2004, the MOD has not defueled any submarines and there is no clear fully funded plan to re-start the work.
The Department has started to dismantle two submarines, Swiftsure and Resolution, but does not yet have a fully funded process to remove, transport and store all types of radioactive parts.
In 2004, the Office for Nuclear Regulation found facilities in Devonport did not meet the latest regulatory standards and the Department stopped defueling submarines.
Following delays, its latest planning estimate, subject to ongoing scrutiny and departmental approval, is to start defueling from 2023 - bringing the process to an 11-year delay.
Overall, the project budget has increased 57% (£100 million), from £175 million to £275 million in June 2018.
The MOD pays an estimated £12 million a year to maintain and store the nine fuelled submarines currently held in Devonport.
There are further issues of space, as Devonport is expected to run out of room for retired submarines by the mid-2020s.
Space constraints have meant the MOD does not have a dock to prepare its most recently retired submarine for long-term storage and is developing other ways of doing this.
Until submarines are placed in storage, they need to be kept partially crewed, potentially affecting the Department’s ability to redeploy its personnel.
From April 2019, the Defence Nuclear Organisation will have responsibility for all disposal-related projects, including those previously within the Royal Navy’s remit.
The Nuclear Legacy Advisory Forum are a group which support local councils deal with nuclear waste, and their chief executive said: " I think there is a desire it seems in the MOD to slightly kick this into the long grass… to deal with the short term costs," said Philip Matthews.
"We know from the NAO report the overall liability is standing at about £7.5 billion for this, and about half a billion pounds has been used up just in sitting these subs where they are in Rosyth and Devonport rather than addressing the issue of the waste that’s within them."
An MOD spokesperson said: "The disposal of nuclear submarines is a complex and challenging undertaking.
"We remain committed to the safe, secure and cost-effective defueling and dismantling of all decommissioned nuclear submarines as soon as practically possible."