Chris McEleny, SNP group leader on Inverclyde Council, is pursuing the Ministry of Defence (MoD), his former employer, claiming he was unfairly targeted over his support for the cause.
Following a preliminary hearing, Judge Frances Eccles was persuaded that Mr McEleny’s backing for independence “has a sufficiently similar cogency to a religious belief... to qualify as a philosophical belief”.
It could therefore be relied upon as a “protected characteristic” for claiming discrimination under the Equality Act 2010.
The case will now go forward to a full hearing.
Mr McEleny’s case centres around his treatment by his former employer when he announced his candidacy for the SNP depute leadership role in 2016.
He was also working as an electrician at the MoD munitions site in Beith, North Ayrshire.
He says that around the time of the leadership hustings he was told that his security clearance had been revoked and he was suspended.
Mr McEleny says he was interviewed by national security officials on issues including his pro-independence views.
He quit claiming he was unfairly targeted for his stance on leaving the UK and his support for the “social democratic values” of the SNP.
During legal proceedings, he cited a previous case, Grainger plc v Nicholson, which focused on a staff member who believed he was made redundant over his belief in climate change, and included written submissions from former first minister Alex Salmond.
Mr McEleny argued his views were “genuinely held”, and “serious, cohesive and important”.
The judgment noted: “The claimant was clear in his evidence that he does not believe in Scottish independence because it will necessarily lead to improved economic and social conditions for people living in Scotland.
“It is a fundamental belief in the right of Scotland to national sovereignty.”
However a lawyer acting for the MoD said there was a significant difference in law between a political opinion or affiliation and philosophical belief.
“It does not have a similar status or cogency to a religious belief,” it was argued.
It was also argued that support for Scottish independence and the SNP does not extend far enough beyond Scotland to warrant the status of a philosophical belief, and it would have “no substantial impact on the lives of citizens in for example Tanzania, Peru or India”.
However, Judge Eccles found that sovereignty and “self-determination” are “weighty and substantial aspects of human life”, and was persuaded that “how a country should be governed is sufficiently serious to amount to a philosophical belief”.
Lawyer Aamer Anwar, speaking on behalf of Mr McEleny, said: “This legal precedent now enables my client to pursue a claim for direct discrimination alleging that he was discriminated against because of this belief.
“But whilst this an unprecedented legal landmark, I am conscious that this case has taken up two years of Cllr McEleny’s life, it really is time that the UK Government launched an inquiry into the alleged treatment rather than forcing him to pursue them through the courts.”
An MoD spokesman said: “It would be inappropriate to comment on the details of an ongoing employment tribunal.”