Two members of the Royal Navy, including one who is due to start work on a Trident nuclear submarine, are members of a far-right group with links to a banned terrorist organisation, the Observer can reveal.

An undercover informant, who infiltrated the UK branch of the pan-European Identitarian Movement and had access to thousands of internal messages, met a Royal Navy sailor who revealed that he was about to take up a posting on a submarine armed with Trident nuclear missiles.

The meeting, involving an informant for anti-fascist group Hope Not Hate, took place at the annual conference of Generation Identity UK in London on 27 July.

The Identitarian Movement, which is fiercely opposed to mass migration, has expanded rapidly in the past two years and has at least 63 “regional branches” of varying sizes across Europe.

The “great replacement” theory was cited as motivation by the mass shooters in the Christchurch mosque attacks, which killed 51 people in March, and the massacre in El Paso, Texas, earlier this month, in which 22 people died.

There is no suggestion that GI UK endorses or supports violence.

Last night the identities of the naval recruit and another GI member serving at the same base were sent to the MoD, which issued a statement saying: “Any extremist ideology is completely at odds with our values.”

The infiltration, coordinated by Hope not Hate, was abruptly terminated after the group’s alleged links to Britain’s nuclear submarine fleet were discovered. “When we realised far-right activists from a group whose stated goal is the ethnic cleansing of Europe were in the navy, we decided to sound the alarm,” said the informant, who has shared the entire cache of internal messages and planning documents of the identitarian group.

The messages show that Generation Identity UK was expelled by the movement’s pan-European network for inviting an antisemite to its recent conference and is now preparing to merge with far-right party For Britain, run by Anne Marie Waters. Prominent supporters of Waters include jailed anti-Islam activist Tommy Robinson.

Facebook Twitter Pinterest Anne-Marie Waters, the leader of For Britain. Photograph: Joel Goodman/Lnp/Rex/Shutterstock

The revelation that the far right has a presence in the armed forces follows the widespread outcry last year when Robinson posed for a photograph alongside a group of military figures.

The informant, whose identity is being withheld by the Observer, added that the recruit he met at last month’s second-ever UK conference of Generation Identity, held in south Kensington, alleged that his membership of GI was widely known in the service. “He says the navy knows he is a member of GI. He claims all the officers are racist,” said the informant, who spent five months inside the group and officially left it as the Observer went to press.

Simon Murdoch, identitarianism researcher at Hope Not Hate, said: “The idea that individuals who subscribe to the dangerous far-right ideology that influenced the Christchurch killer are serving members of the Royal Navy, and that one claims to be taking up a job on a nuclear submarine, is completely unacceptable and actually quite terrifying. We simply cannot allow this dangerous ideology to gain any traction within our armed forces.”

A YouTuber who had links to National Action before it was proscribed as a terrorist group by the Home Office in 2016, spoke at last month’s London conference, although the speech was not recorded, at the organisers’ request. The informant claimed the speaker had also invited two National Front members who were also former members of National Action and were identified by a GI regional leader.

Previously, Jacob Bewick, an activist with GI, had been exposed as a member of National Action and was spotted at an NA march in 2016. At the conference, one GI UK member told the informant that two members of the fascist National Front were also believed to be former National Action recruits.

While Generation Identity UK disavows violence and neo-Nazism, internal correspondence, sent on encrypted messaging app Telegram, reveals racism and antisemitism. They show that the UK branch has been expelled from Europe’s large identitarian network after recently inviting antisemitic white supremacist Colin Robertson – aka Millennial Woes – from West Lothian to its conference last month.

Martin Sellner, the Austrian leader of Europe’s Generation Identity movement, wrote to fellow leaders, that he would “disavow the English movement publicly and declare that it is no longer part of GI, demanding to change its name and branding” after its unauthorised invite to “alt-right YouTubers, whose positions do not represent us”.

Robertson has described himself as “pro-slavery” and called for the torpedoing of refugee boats.

In June, Sellner himself was permanently excluded from entering the UK by the Home Office, which assessed that the 30-year-old posed a serious threat to the UK’s interests of preventing social harm and countering extremism.

Another speaker at the conference was Waters, who has described Islam as “evil” and has attracted 34,000 Facebook followers to her group.

Last night, an MoD spokesperson said: “It would be inappropriate to comment specifically on these allegations. We take allegations of this nature very seriously and would always carry out investigations into such matters when they are made against service personnel.”