Britain's Trident nuclear submarine bases at Faslane and Coulport on the Clyde will in future be run by private companies, the Ministry of Defence has disclosed.

The ministry has signed a 15-year contract with AWE, the consortium which already operates the Atomic Weapons Establishment at Aldermaston in Berkshire, where nuclear warheads are designed and maintained. Additional contracts have been signed with Babcock and Lockheed Martin, part of a new consortium to be known as the ABL Alliance.

The consortium will be responsible for the day-to-day running of the Clyde bases, according to officials. The MoD will rely increasingly on skilled and specialist staff from outside the ministry, they added. The ministry and the navy face a shortage of skilled personnel as existing specialists retire.

As part of the agreement, 149 MoD civilian posts will be transferred, and 39 Royal Navy posts seconded, to the ABL Alliance, the MoD says.

In a reference to Aldermaston, it describes the new agreement as "a natural extension of [the companies'] current role in supporting the nuclear warhead carried by our Trident missiles".

The AWE at Aldermaston is run by a consortium of Jacobs Engineering Group, Lockheed Martin UK and Serco, which have a 25-year contract to operate it until March 2025.

The deal covering the Trident bases on the Clyde comes as the MoD presses ahead with ambitious and controversial outsourcing plans. Its move to privatise the multibillion-pound agency that provides the armed forces with military equipment were criticised by a leading security thinktank for being ill thought-out and potentially dangerous for British troops.

"History is littered with outsourcing deals that either or both parties eventually find constraining and/or, in practice, more expensive," said the Royal United Services Institute report. "After the G4S and Olympics episode, the privatisation of the railways is the most obvious example of this, but there are many others."

It said the outsourcing plan suffered "from an inherent weakness, since it appears to rest on an argument that, because the government is not very good at negotiating and managing contracts with the private sector, it is going to negotiate an even bigger contract with a private-sector entity to undertake the entire task on its behalf. Persuasive arguments against this logic need to be marshalled."

The MoD says it engaged "extensively" with trade unions about the Trident bases contract, which is intended to come into force in January 2013.