The Department of Transport has the widest gender pay gap of any government department, with women earning 16.9% on average less than male colleagues.
Women are paid less than men across the civil service, new figures show, with a gap of 10% in seven other departments.
The lowest disparity is 3% – in the culture, media and sport department.
The UK’s top civil servant Sir Jeremy Heyward said the data was a “matter for concern” but he hailed a fall in the overall pay gap from 13.6% to 12.7%.
The civil service, which employs 419,000 staff, compares favourably with the public sector as a whole, where women are paid on average 19.4% less than men and the private sector where the figure is 23.7%.
All government departments are now required to publish an annual gender pay audit under regulations introduced by Theresa May earlier this year applying to all public bodies with 250 or more employees.
The figures show the following gender pay gaps between men and women in various departments:
- Department for Transport: 16.9%
- Department for Exiting The EU: 15.26%
- Department of Health: 14.2%
- Ministry of Defence: 12.5% (for civil servants)
- Department for Business, Energy and Industrial Strategy: 12%
- Department for the Environment, Food and Rural Affairs: 11.5%
- Foreign and Commonwealth Office: 10.6%
- Home Office: 10.1%
- Department for Culture, Media, Digital and Sport: 3%
Officials in the department of transport said it had traditionally been a “very male-dominated environment” but progress was being made and they believed there was “equal treatment for work of equal or similar value”.
“There is a disproportionate representation of men due to the technical, engineering, construction and maritime skills required and lower proportions of female students in STEM (science, technology, engineering and maths) subjects leading into those careers,” said permanent secretary Bernadette Kelly.
Sir Jeremy, the cabinet secretary and head of the civil service, said he was committed to improving the gender balance at all grades within the civil service.
“I am pleased to say that the overall civil service gender pay gap is narrowing although it is still a matter of concern,” he said.
But the FDA union, which represents senior civil servants, said that it was wrong that women were still being “discriminated against and undervalued”.
“While the civil service should be applauded for shining a light on its gender pay gap with this latest data, departments have a long way to go if they are serious about closing it,” said its equality officer Zohra Francis.