The council introduced a scheme that harmonised terms and conditions for white-collar and manual staff. It was agreed by Unison and MPO.
But school-based staff, home carers and some DSO staff were excluded.
A GMB circular to members said there was 'a strong case for believing that their treatment of some DSO employees could constitute unlawful sex discrimination.'
A council spokesman said Milton Keynes had a complex range of conditions as a hangover from reorganisation, but was working towards including remaining groups of staff.