It says the full picture of what is happening in the programme is hidden from public view, and claims that the true cost is likely to be in the region of £172bn between now and 2070.
That figure is far greater than the Ministry of Defence's (MOD) estimate of £31bn plus a £10bn contingency for building four new Dreadnought submarines.
The department also believes the service costs of the nuclear deterrent will be similar to now - around 6% of the annual defence budget.
The MOD also says it expects to invest more than £50 billion on Nuclear Enterprise equipment and programmes over the next nine years.
The Nuclear Information Service says delays to weapons upgrades and escalating costs could eventually have an impact on the Continuous At Sea Deterrent (CASD).
It predicts the Government could eventually be faced with a choice between paying for project upgrades at the expense of other public spending priorities, or abandoning submarine-based weapons systems altogether.
David Cullen, Director of the Nuclear Information Service, said:
"Our report lists a large number of risks to the programme - there are 21 we have identified.
"The way that some of those risks are interdependent, and problems in one area can cause problems in another, I think causes serious doubt that the MOD will be able to deliver the progamme to budget and on time in the way that they say."
The Ministry of Defence has said:
"Our nuclear deterrent protects us from the most extreme threats to our security and the Government is committed to delivering it as efficiently and cost-effectively as possible."