It was claimed the documents suggest South Lanarkshire Council paid about 90% of a key group of male manual workers more than female counterparts assessed as having the same skill levels.
About 580 male gardeners and refuse collectors should have earned between £8.77 and £9.17 an hour at today's rates, the same as about 2000 female carers, cooks, classroom assistants and school clerical workers on the same job grade.
However, about 530 of the men were paid more than £9.17 an hour through unfair bonuses and secret pay deals, and about 400 were paid more than £10.07 an hour, according to campaigners.
South Lanarkshire, which has 4400 male staff and 10,400 female workers, now faces a multi-million-pound compensation bill from women who may have been illegally underpaid for years.
Labour's Eddie McAvoy, who has run the council since 1999, faces calls to resign.
The council is already being taken to a tribunal by 3000 female staff claiming more than £10 million in back pay, with a hearing due in October.
Its latest accounts admit many of these claims could be backdated up to five years from the date of the original grievance, and that if it loses a large number of the cases it faces a very substantial loss.
The SNP last night demanded "full disclosure" from McAvoy on the scale of the problem.
The figures have emerged from a long-running freedom of information (FoI) case launched in 2010 by equal pay campaigner, Mark Irvine.
In light of many other councils paying male staff more than female peers, and being forced to pay compensation, Irvine asked South Lanarkshire about male workers on the "LSO3" grade. In theory, women should have been paid the same as the men on LSO3, but in practice almost all of the men got more, the files indicate.
The council only released the data under FoI after losing an appeal to the UK Supreme Court last month.It had previously refused to release the figures when ordered to do so by the Scottish Information Commissioner and the Court of Session.
The Supreme Court appeal, the first by a Scottish public body in an FoI case, is likely to cost the council £200,000 in legal fees.
However, evidence of widespread and systematic unfair pay could cost it tens of millions more.
South Lanarkshire SNP councillor Peter Craig said: "There has now got to be full disclosure. There are huge sums of money at stake."
A South Lanarkshire Council spokesman said: "All council employees are paid in accordance with their evaluated rate, regardless of gender.
"Mark Irvine's analysis is inaccurate - it ignores additional aspects of pay which are included in employees' salaries, such as shift working and overtime."