Thousands of low-paid female workers at Scotland’s largest council are set to share in a windfall believed to be worth up to £50 million after earning victory in a long-running pay dispute.

The Court of Session rules that women in Glasgow had been excluded from sizeable bonuses for many years. Unions had argued that while the claimants had been unfairly discriminated against before the new system was introduced a decade ago, the city council’s decision to continue the unequal pay was also discriminatory as it excluded women claimants from pay protection.

Around 6000 claimants are understood to be affected by today's decision. It is still unclear what the scale of the payouts will be or the impact on the authority's financial position. The new SNP administration on the council had made a manifesto commitment to resolve all outstanding equal pay disputes. Unison, Scotland’s largest public service union, said it represented 1400 claimants, many of whom had equal pay claims dating back to 2006.

Union sources said the payouts from this case alone will cost the city council tens of millions of pounds, with one citing a figure "of at least £50million".

One said: "The old regime resisted what had been decided in other cases across the UK from 2009, while new administration indicated during the local government election that they would address the issue. This has been repeated since and we look forward them holding to that through early discussions."

The Herald also understand the only avenue open to the city council to challenge the decision is to take the case to the European Courts.

The Court of Session has also been asked to consider whether the current council pay system is a valid pay scheme.

Mike Kirby, Unison's Scottish Secretary, said: “The pay protection win is great news. The way Glasgow rates and pays workers has been the source of conflict and division for ten years. These women have already waited long enough to receive the pay they have worked hard for and deserve. It's time for Glasgow City Council to do the right thing and pay up on equal pay.”

Suzanne Craig, UNISON’s legal officer, said: “I am delighted that the Court of Session has ruled in favour of our women members. It also sends a clear message to Glasgow City Council that it cannot continue to defend these discriminatory practices any longer.

“This decision will deliver money for women who should have been paid more before single status and were then excluded from pay protection after single status.”

Glasgow City Council is yet to respond.

A decision on a second, more significant, challenge by Unison to Glasgow's overall workforce, pay and benefits system is currently going through the Court of Session.

The union had challenged the council’s method of measuring the value of jobs, in particular the use of different scales, one for core pay and others for non-core pay.

Unison had argued the system made it impossible for employees to know if they were being paid equal.