City of Lincoln Council paid men 18% more than women, government figures show.
The council submitted its pay gap data showing that women get 82p for every £1 that men earn.
Figures also showed that around 44% of the council’s top earning staff were women.
Meanwhile, Lincolnshire County Council submitted a gender pay gap of 13.3%.
Of the county council’s highest paid employees, 55% were women.
The authority also recorded a mean bonus pay of 19.8% lower for women than men.
Angela Andrews, Chief Executive of City of Lincoln Council, said: “We are an equal opportunities employer and we ensure all our staff are treated fairly. We pay employees equally for the same roles, regardless of their gender.
“Any apparent pay gap is the result of the variety of jobs undertaken by men and women and the salary that these roles attract.
“We ensure our policies and procedures are fair and support a work-life balance for all. We also offer the opportunity for flexible working and monitor our workforce data to identify any trends and actions required.”
Lincolnshire County Council were approached for comment but had not responded by the time of publishing.
It comes as companies and organisations are submitting their gender pay gap data to the government.
Firms with 250 employees or more are required to submit the difference in pay between male and female employees.