Equal pay campaigner Mark Irvine said South Lanarkshire Council paid a 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 the same as about 2000 female carers, cooks, classroom assistants and school clerical workers on the same job grade.
However, Mr Irvine said about 530 of the men were paid more than £9.17 an hour through unfair bonuses and secret pay deals, including 400 paid more than £10.07.
South Lanarkshire, which employes 4400 male 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, council chief since 1999, faces calls to resign.
The council is already being taken to tribunal in October by 3000 female staff claiming more than £10 million in backpay.
The SNP last night demanded full disclosure from Mr McAvoy.
The figures have emerged from a Freedom of Information case Mr Irvine launched in 2010 following similar situations in other councils.
The council only released the data after losing an appeal in the UK Supreme Court last month.
The council is likely to pay about £200,000 in legal fees.
A South Lanarkshire Council spokesman said: "Mark Irvine's analysis is inaccurate - it ignores additional aspects of pay which are included in employees' salaries, such as shift working and overtime."