MINISTRY of Defence insiders questioned whether an SNP councillor should keep his job four years before his security clearance was revoked, leaked emails reveal.

Inverclyde Council’s Chris McEleny was also suspended when his permissions were removed in 2016.

That decision was taken after he announced he was running in the SNP’s depute leadership contest, and saw him quizzed over his opposition to Trident and views on Irish politics.

McEleny, who has Irish heritage, was working for the MoD as an electrician at the time and was reinstated two months later, before ultimately leaving altogether.

He launched a discrimination case against his former employer in 2017. The process is set to go to a full hearing after a judge dismissed MoD arguments that McEleny’s independence belief was not a philosophical position and so could not be covered by anti-prejudice laws.

Now evidence has emerged that figures within the MoD began asking questions about whether or not McEleny should keep his job as far back as 2012.

A source told The National: “It doesn’t look too good for the MoD.”

In emails seen by The National, concerns were raised by personnel from HMS Neptune – the name given to the shore facilities at HM Naval Base Clyde, home to the UK’s nuclear deterrent – in a message dated October 2012.

It was sent after McEleny addressed that year’s SNP autumn conference.

Marked “Restricted – Need to Know only” – it states: “I have just been made aware of a speech that Mr C McEleny gave at the recent SNP conference in his position as an elected SNP councillor.

“The speech is openly available for download on U tube. During the speech Mr C McEleny clearly states his ‘anti nuclear’ position, his support for an independent Scotland Naval Base in Faslane and the fact that he is currently an employee within HMNB Clyde.

“I do not know if he has declared the fact that he is an SNP councillor

to DBS NSV [the unit that vets defence employees and contractors]. However, when questioned, they have stated to my staff that they have an open file on this individual at the moment (dating back to 2004).

“Is there a conflict of interest here? Should we be concerned about his continued employment?”

In a reply several days later, the respondent wrote: “Given that membership and activities associated with the SNP are not illegal you should be extremely careful before considering any action on what is a legal activity. It will almost certainly be up to his line manager... to decide whether his stated political beliefs makes his continued employment in his current post still tenable.”

Last night, the MoD said it could not comment due to the ongoing tribunal. A date for the full hearing has yet to be published.

However, official guidance on political impartiality from the civil service code states that those employed by the MoD must serve the government regardless of their own political beliefs, “act in a way which deserves and retains the confidence of ministers” and ensure they do not allow their personal political views to determine their actions or any advice given.

Commenting on the emails, McEleny said: “This is part of an ongoing employment matter so as alarming and concerning as this is, it would be inappropriate for me to comment until after the completion of the process.”

A solicitor for the MoD had argued that the case should be thrown out as ideals around Scottish governance did not extend far enough beyond the country’s borders to warrant the status of a philosophical belief and would have “no substantial impact on the lives of citizens in, for example, Tanzania, Peru or India”.

However, this was dismissed by Judge Frances Eccles.