A statement from NHS Fife said the fact there were more women who were having children and choosing to work part time was responsible for their low levels of medics.
Bosses, controversially referring to the “feminisation” of the workforce, said maternity leave “added pressure” in certain departments such as paediatrics.
But Scottish Labour said the claims were “unacceptable in this day and age”, and patients groups said they would undermine staff morale.
At an annual health review last week, a statement from the board that was passed out at the meeting said NHS Fife faced “major challenges”.
It added: “These 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 lead to an ongoing impact in some specialties (particularly paediatrics) and solutions need to be worked through both regionally and nationally.”
In addition, an NHS Fife report on their workforce released in June this year 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.”
Labour MSP for Cowdenbeath in Fife, Helen Eadie, said: “This 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.”
She continued: “I find it objectionable that the term ‘feminisation’ of the workforce is used.
“To single female employees out is not acceptable.
“All employees present opportunities and challenges and all employees deserve to be valued so what sort of message does this send out to NHS Fife workforce reading messages like this in the public domain?”
She continued: “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 so why single out women?
“Where are the stats on those men who undertake such a role?”
Dave Leung (corr), founder of Fife Patients Association, said the statement might further undermine morale of the health board’s female workers.
He said: “It’s just ridiculous in criticising 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.
“I think 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.
“The fact is the SNP has cut nurses by more than 2000 in the last couple of years, and no amount of jargon can hide that fact.
“Patients will find it hard to believe that a health board can conjure this excuse for the words being understaffed.
“The Scottish Government has its health budget protected, so we need firm answers as to why NHS boards are feeling the need to make excuses like this.”
A report earlier this year said 48% of medical and dental staff in Scottish NHS hospitals, communities and public health services staff were women.
NHS Fife Medical Director, Dr Brian Montgomery, said: “We did not say that ‘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 an extremely positive development, referred to as feminisation of the workforce. These comments have clearly been taken out of context.
“Women also have the right to choose to have families however it is well recognised that maternity leave and part-time working imposes an additional pressure on availability of trainee doctors.
“We continue to work towards finding ways to accommodate these choices by being flexible with our workforce whilst maintaining services for our patients.”