Caroline Flint, a state secretary for Europe in the Foreign Office, made her remarks in a resignation letter after she was reportedly passed over for promotion in Friday's reshuffle.
"You have a two-tier government - your inner circle and then the remainder of Cabinet," she said. "I am extremely disappointed at your failure to have an inclusive government."
Flint, one of the 101 women who became known as "Blair Babes" after winning parliamentary seats in the 1997 landslide election victory of Tony Blair, served six years in government.
She is a friend of Hazel Blears, the communities secretary who triggered the current flood of resignations from the Brown cabinet with her decision to step down last Tuesday.
Following a reshuffle undertaken by Brown Friday, the number of female full cabinet members in the 23-strong cabinet has dropped to just three.