Dr Sally Winning, deputy chairwoman of the Scottish Council of the British Medical Association, said poor workforce planning was responsible for NHS Fife's problems, not its female employees.
She agreed with Labour MSP Helen Eadie the comments, made as part of their performance review, were offensive.
Dr Winning said: "I think it really shows the Fife board in a very bad light. They have failed to plan appropriately. They know when they employ people the proportions of their workforce. They have access to workforce trends information across the whole of Scotland and should be able to predict and plan for part-time work and periods of maternity leave."
The growing number of women studying medicine at university and training to become specialists has been noted in Scotland for a number of years.
Dr Winning, who as a single mother became the first person to train as a psychiatrist part-time in Aberdeen 18 years ago, said some boards had creative solutions for staff juggling careers with child care.
However, she said she knew some doctors had found health boards too rigid when it came to flexible working proposals.
The statement made by NHS Fife had said: "Challenges have been compounded by the feminisation of the training grade workforce and legislative and other changes which have made recruitment of locum staff difficult.
"The increased female medical workforce imposes an added pressure on availability of trainee doctors due to maternity leave and part-time working."
NHS Fife medical director Dr Brian Montgomery said: "Recent admission figures for Scottish Medical Schools now show the majority of entrants are women. As previously said, this is a positive development."
NHS Fife director of human resources Rona King said: "NHS Fife does not accept there has been a failure of workforce planning. It participates in national workforce planning led by the Scottish Government to ensure there are the correct number of staff with the right skills available."