NHS Fife's statement was branded "deeply offensive" by the Scottish Labour Party after it suggested the rise in females having children and working fewer hours was responsible for its low levels of medical staff.
The board referred to the "feminisation" of the workforce and said maternity leave "added pressure" to departments such as paediatrics.
Labour said the claims were "unacceptable in this day and age", and patients' groups said it would undermine staff morale.
The claims were made at an annual health review when NHS Fife admitted it faced "major challenges".
A statement 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.
"This has led to an ongoing impact in some specialities (particularly paediatrics) and solutions need to be worked through both regionally and nationally."
In addition, an NHS Fife report in June said: "Feminisation of the medical workforce has led to capacity issues within some areas, as a result of periods of maternity leave and accommodating part-time working."
Helen Eadie, Labour MSP for Cowdenbeath in Fife, said: "It is unacceptable in this day and age to infer criticism of women in the workforce and I find it deeply offensive to families all over NHS Fife's workforce.
"I find it objectionable that the term 'feminisation of the workforce' is used. To single out female employees is not acceptable. All employees present opportunities and challenges, and all employees deserve to be valued.
"The problems faced by NHS Fife are not to do with so-called 'feminisation' but a simple reduction in the numbers of medical training posts.
"There are myriad reasons why staff have time off work. In this day and age many fathers play an increasing role in the care of children. Where are the stats on those men who undertake such a role?"
Dave Leung, founder of Fife Patients' Association, said the statement might undermine morale of the health board's female workers.
He said: "It's just ridiculous to criticise the female side of the workforce. It's just another example of mismanagement.
"There is poor morale in female staff. We've been contacted by a number of nurses saying management is distant from what's on the ground.
"[Chief Executive] John Wilson doesn't seem to have grasped the issues. The issues are the allocation of resources – there's not enough doctors and nurses – and the allocation of funds.
"This is poor human resources management, it just doesn't seem to connect with the staff."
Scottish Conservative health spokesman Jackson Carlaw said: "Since time began, healthcare has always been made up of predominantly women, so this 'feminisation' line is hardly new. Neither is the likelihood of females having children or requiring to work part time, so this sounds like a hugely dated – and desperate – excuse."
NHS Fife medical director Dr Brian Montgomery said: "We did not say female workers 'give us a headache'.
"We have acknowledged there has been an increase in the number of women choosing a career in medicine. This is a positive development, referred to as feminisation of the workforce. These comments have been taken out of context.
"Women have the right to choose to have families, however. It is recognised maternity leave and part-time working imposes an additional pressure on availability of trainee doctors."