Funding of £2bn was allocated for rebuilding facilities between 2005 and 2015 at Berkshire's two Atomic Weapons Establishment (AWE) sites.
AWE had spent £3.96bn by the end of the 2015/16 financial year, a Freedom of Information (FoI) request has revealed.
An AWE spokesman said the money spent was part of "annually agreed funding".
Three out of five planned projects at the sites in Aldermaston and Burghfield were completed on time in 2015.
However, the Ministry of Defence's (MoD) response to the FoI revealed that AWE was now expected to complete projects Pegasus and Mensa in 2020.
Pegasus will store and handle enriched uranium components for nuclear warheads, and Mensa is where the weapons will be assembled.
The MoD said providing estimates on how much money had been spent this year and in the future would "compromise" its negotiating position.
An AWE spokesman said: "The figures released by the MoD, in response to the recent Freedom of Information request, form part of our annually agreed funding from government, ensuring our capability in support of the UK's nuclear deterrent.
"This funding covers the capital costs of a complex nuclear licensed site and replacement nuclear facilities, all of which is subject to rigorous scrutiny."
Newbury MP Richard Benyon, whose constituency includes AWE, said the delays were "bad news for the taxpayer".
He added that he believed procurement processes at the MoD were improving and resulting in reduced expenditure.
An upgrade of the UK's Trident warhead factory has cost double its budget - and it is expected to take more than two further years to complete.