Concerns about Trident raised by Royal Navy submariner William McNeilly were either incorrect, the result of misunderstanding or based on historic events, and safety has not been compromised, Defence Secretary Michael Fallon has said.

Mr Fallon said a Ministry of Defence (MoD) investigation into claims made by Able Seaman McNeilly has found that neither the operational effectiveness of Trident nor the safety of the public or submariners have been compromised.

The 25-year-old sailor went absent without leave earlier this month after producing an 18-page report containing a series of allegations about the Trident submarines based at Faslane on the Clyde in Scotland.

Mr Fallon said McNeilly is being confined to a "specified location" in Portsmouth where he is being interviewed and is being "afforded the duty of care that we give all our personnel".

In a written ministerial statement, Mr Fallon said: "Having now completed our investigation, and having consulted with the appropriate regulatory and operating authorities, I can assure the House that neither the operational effectiveness of our Continuous at Sea Deterrent nor the safety of our submariners or members of the public have been compromised."

The Defence Secretary said that only one of Able Seaman's McNeilly's claims, that e-cigarettes are being used inside submarines, needs to be investigated further but there is "clear evidence" that their use does not but the safety of the boats at risk.

Mr Fallon said: "Most of McNeilly's concerns proved to be either factually incorrect or the result of mis- or partial understanding; some drew on historic, previously known, events none of which had compromised our deterrent capability and, where appropriate, from which lessons had been learned to develop our procedures as part of a continuous improvement programme.

"Only one of the allegations remains to be fully examined - the allegation that e-cigarettes were being used within the submarine.

"No independent corroboration of this has been found but even if it were true, there is clear evidence that their use did not put the safety of the boat at risk.

"Able Seaman McNeilly was arrested having not reported for duty after a period of leave.

"He was released the next day, but confined to a specified location in Portsmouth while interviews were conducted.

"He is being afforded the duty of care that we give all our personnel, is in contact with his family, and is still in the employ of the Royal Navy."

Mr Fallon said that if Able Seaman McNeilly had raised his concerns with colleagues or the chain of command, more experienced and senior submariners would have explained that his fears were unfounded.

The Defence Secretary said: "Able Seaman McNeilly published his comments following his first submarine deployment.

"He was under training, and his access and exposure to activities and material on board were appropriate to his security clearance.

"We have found no evidence that he raised any concerns with colleagues on board or with the Chain of Command: had he done so, the more senior and experienced submariners would have been able to explain how the boat operated and why McNeilly's concerns were unfounded.

"A number of the issues he raised did not occur during his patrol."

Mr Fallon added: "The Naval Service operates its submarine fleet under the most stringent safety regime, which is subject to independent scrutiny.

"The Naval Service does not put a submarine to sea unless it is safe to do so, and there are appropriate procedures in place to deal with any issues that may arise during its deployment.

"There are robust regulatory mechanisms, both within the Ministry of Defence (MOD) but independent of the Royal Navy and, externally with the Office of Nuclear Regulation, to ensure this. The MOD is also held to wider account by Parliament."

In his report, which was published online and also sent to newspapers and journalists, McNeilly said he was an engineering technician submariner who has been on patrol with the Trident submarine HMS Victorious.

He claimed there are fire risks and leaks on board and security checks are rarely carried out on personnel and contractors working on the submarines when they are docked at Faslane.

He also alleged that alarms were muted because they went off so often, missile safety procedures were ignored and top-secret information was left unguarded.

McNeilly, originally from Newtownabbey, County Antrim, said he raised concerns with senior officers but decided to publish his claims because they were ignored.

He wrote: ''Our nuclear weapons are a target that's wide open to attack.

''It is just a matter of time before we're infiltrated by a psychopath or terrorist.''