NHS Fife is to stipulate from next month that both partners in a couple seeking IVF treatment should be non-smokers.
Two other health boards, NHS Forth Valley and NHS Borders, have the same requirement.
According to NHS Forth Valley, which updated its guidelines in June, smoking by either partner "significantly" reduces fertility.
However, at least nine of Scotland's 14 health boards, including Greater Glasgow and Clyde, Lanarkshire, Grampian and Tayside, accept couples on to the waiting list where either or both partners smoke, although patients are strongly advised to stop before treatment. NHS Lothian requires the female patient to be a non-smoker.
A spokeswoman for NHS Fife said: "We maintain our decision that both partners are non-smokers due to the risks associated with passive smoking."
Dr Brian Montgomery, NHS Fife medical director, said: "If a woman smokes or is exposed to secondary smoke there is an increased likelihood that IVF treatment may be unsuccessful.
"Furthermore, smoking or exposure to secondary smoke carries well-recognised risks for both the unborn child and the mother. Stop-smoking support is available from couples across the three community health partnerships in Fife."
NHS Forth Valley's policy on the treatment of sub-fertile couples states: "Cigarette smoking, including passive smoking, has been proven to significantly reduce fertility and delay conception."
The British Medical Association Scotland gave a more qualified response. A spokeswoman said: "The decision of whether or not to proceed with fertility treatment should be a clinical decision based on the likelihood of success.
"If there is clinical evidence that smoking, for example, means that fertility treatment would be less effective, then it could influence the decision-making process.
"However, people's lifestyle choices or behaviour in itself shouldn't form the basis of a decision on treatment."
Simon Clark, of smokers' group Forest, said denying medical treatment to people on the grounds they smoked was opening a can of worms: "Where do you stop? People who are obese or drink heavily?"
Infertility groups have been campaigning for years about the wide variation in the sort of IVF service on offer in different health board areas. They are concerned boards acting now to change access criteria are pre-empting the submission of a report to the Scottish Government by the National Infertility Group, due in December.
The group was set up in 2010 to make recommendations on how to make fertility services around Scotland more consistent. Part of its remit has been to look at standardising access criteria, including in regard to patients who smoke.
NHS Fife said it was necessary to introduce its changes to access criteria now "to begin to reduce the current waiting time of three years and improve the outcomes".
Gwenda Burns, of Infertility Network Scotland, strongly criticised NHS Fife for changing its rules before publication of the report. She added: "We're not against criteria on smoking being brought in if it's medically based – and smoking, as everyone knows, isn't healthy – but we want to know what help is going to be given to people to help them quit."
A Scottish Government spokeswoman said: "IVF guidelines are currently determined by each individual NHS board; however, the National Infertility Group will make recommendations to ministers in December 2012 on standard access criteria for all NHS boards, to ensure equal access across the country."