The 13% pay gap is only partly explained by women's family commitments.
Men earned £83,333 on average in 2006, while women earned £72,250.
In The Pay Gap for Women in Medicine and Academic Medicine, co-published with the BMA, the Medical Women's Federation (MWF) suggested that women are reluctant to bargain to increase pay.
Academic research hints that ‘women are poor or unwilling negotiators', the report said.
Dr Clarissa Fabre, MWF president-elect and a GP in Uckfield, Sussex, agreed: ‘Women do not like to bring up money or for example, time to parity.
‘It's in their nature not to ask. They want something that's convenient for their lives. Men are much more forward about it.'
The MWF said half the pay gap is explainable. Men's earnings outstrip women's because they are more likely to take on extra work, Dr Fiona Cornish, a Cambridge GP, said.
‘In my own practice there are three women and two men. We all earn exactly the same rates but the men do far more out-of-hours.'
GPs made up 6% of the sample of 1,162 doctors who completed a pay survey of women in academic and clinical medicine.
Office for National Statistics figures show that the official national gap is 12.2% and that it narrowed from 12.6% last year.
- Read the full version of this story in next week's edition of GP dated 20 November.
- Do you think it's right that male GPs earn more than female?