The Very Reverend Lorna Hood, last year's Moderator of the General Assembly of the Church, revealed she was told she would "not be welcome" in some parishes in the Lochcarron and Skye presbytery during a visit as part of her duties in the year-long ambassadorial role.
Yesterday, at the annual gathering of more than 700 ministers and elders in Edinburgh, another former Moderator, the Very Rev David Lacy, called on the Assembly to act and urged women who have been discriminated against to come forward.
He said for the Moderator to be faced with sexism in the presbytery was a "slap in the face to the court (of the General Assembly)".
Rev George White, Principal Clerk to the General Assembly, told Mr Lacy the first stage of any push must take place with complaints being lodged at local level. It is understood this could be done on behalf of individuals who feel discriminated against.
Members of the Lochcarron and Skye Presbytery said only a small number had objected to the Moderator's visit and that she had received strong support from many during her visit.
Blocking women in such roles breaks the Church laws that have allowed female ministers since 1968 and female elders since 1964, and its 2007 broader anti-discrimination law.
Mr Lacy said sexist ministers and elders should modernise or leave the Kirk. When questions are asked it is claimed no females have been proposed, he said.
The alleged practice of refusing women roles in the Church at local level in some areas - mostly on the west coast but also in pockets of the Central Belt - shocked Mrs Hood.
Mr Lacy, who was Moderator inbetween 2005-6, said: "I think there are ministers and elders who are not representative of the majority, but they are powerful grumbling grunters who have to decide if they are in the Church of Scotland.
"If they are in the Church of Scotland they should put their toe to the line. I think youngsters see through the antiquated gangsterism of it all."
He went on: "Those ministers and elders who break the law of the Church should be taken to task by the local presbytery and if they don't obey their presbytery it should come to the Assembly."
Mrs Hood said she was warmly welcomed by those she saw during the August presbytery visit, one of four she carried out during the year.
But she said: "It was a shock to be told there were only certain pulpits I would be welcome in, that my preaching in Skye was restricted to three parishes at the top of the island, where I was given a wonderful welcome.
"In Portree I was the first woman to ascend the pulpit steps. And you know the roof was okay ... (it) didn't collapse."
She added: "What did concern me, however, was the number of women who spoke to me of their pain and sorrow. Some were in tears."
Around 20 to 30 of the Kirk's 1389 congregations are thought to have no female elders, but "that's too many", said Mrs Hood.
Ministers and elders are chosen after a series of proposals and discussion by Kirk Sessions, made up of senior members of the parish. Appeals go to presbytery before the General Assembly.
Mr Lacy, who described the accusations of sexism as "flagrant disobedience", said he expected the issue to be raised fully at next year's Assembly.
Steve Fennell, an elder at Kilmore Parish Church in Sleat, Skye, claimed only a small number of ministers in the south of the presbytery area were opposed to Mrs Hood. He said: "I felt extremely embarrassed and that was why I today gave Lorna Hood a hug because she knew a lot of us were hurt.
"It is not just the fact some ministers are women, a lot of the Kirk Sessions will not accept women elders. We would love to have women elders."
Mrs Hood preached at Portree Parish Church, led by the Rev Sandor Fazakas, during her visit.
Mr Fazakas said: "About 25 people from other parishes came up to Portree to attend the worship Lorna was conducting.
"They told her how regrettable it was she was not able to visit their congregations when everyone would be delighted to see her."
Figures reported earlier show in 2012 there were more female elders than male in the Kirk, with a total of 17,202 women, against 16,936 men.
In Lochcarron-Skye presbytery, there were 12 female elders and 30 male elders.
Jenny Marra, Labour MSP for North East Scotland, welcomed the step towards greater equality. She said: "The more women that are represented in all our institutions in Scotland then the better decisions are made."