An Amnesty International UK bookshop manager is taking the organisation to an employment tribunal over claims she was paid less than a male colleague for doing the same job.
Ailsa Dixon, manager of Amnesty International UK's Edinburgh shop, brought a grievance against the human rights organisation, which campaigns for women's rights, last year.
According to The Times, she worked four days a week for pay that would have been £24,000 if she had worked full-time, while a male colleague running another branch on a five-day contract received £28,000.
A spokesman for the trade union Unite, which is representing Dixon, said: "Unite is supporting a member who has an equal pay issue and the case is now set to progress to an employment tribunal hearing. As such it is not appropriate to make further comment at this stage."
An Amnesty International UK spokesman said the complaint was about the grading of roles and it had "followed our robust internal policies and procedures to look into the matter".
The spokesman added: "We have now concluded our internal process, including an appeal process, and the concerns were not upheld.
"Although the article mentioned that the individual concerned is planning on taking this to an employment tribunal, we have yet to receive any notification of this, so we can’t comment on that at this stage.
"It is also disappointing that the journalist did not mention that Amnesty International UK has a median gender pay gap of 0.0 and a mean of 0.7."
The dispute comes at a time when Amnesty International UK management and Unite have just settled a long-running pay dispute.
The Amnesty International UK spokesman said: "Management and the union now have an agreed pay and grading structure after a vote by members that concluded on Tuesday night."
He said the two parties "worked together at every step of the process" and this was the first time in more than 10 years that the pay and grading structure had been comprehensively reviewed.
The Times claimed the new pay deal might mean that some workers would have their jobs regraded and their pay cut while some senior managers enjoyed pay rises of more than 10 per cent.
The Amnesty International UK spokesman said it "has been committed to pay at the median of the sector for a number of years and the process involved evaluating and benchmarking all the jobs at Amnesty International UK against the market".
He added: "All grades will now be paid at or above the benchmarked median for the sector. The senior management team will be paid at the median for the sector."
Unite regional officer Alan Scott said: "Throughout the negotiations Unite has made clear its opposition to the inequitable and disproportionate pay for senior staff, to the principles of benchmarking to the market median and the broken promise made around staff not losing pay.
"Management and the board chairs made clear their unwillingness to shift from these positions and members have voted with the knowledge of this position and how it would affect the resolution and proceedings of these negotiations."