Elsie Houston was a guide at Glasgow Cathedral for 30 years before she died aged 87.
John Turner was asked by her family to play the music written by her late husband, the Rev Freddie Houston.
But the Church of Scotland said he could not for legal reasons connected to employment contract obligations.
However Mrs Houston's daughter, Margaret, said she believed organists' contracts should not have been a barrier to letting a heir family friend play the Mr Houston's compositions, which only Mr Turner knew intimately enough to perform properly.
Miss Houston said her father, who was minister at Townhead and Blochairn in Glasgow for nearly 30 years, had steered Mr Turner through the nuances of his compositions and her mother had specifically asked him to recreate the music she had loved.
Miss Houston said the family was shocked to be told two days before the funeral two weeks ago that Mr Turner would not be allowed into the organ loft.
Mr Turner said he was "disturbed" at claims the ban was imposed for any legal reason.
He was involved in an employment dispute with the Church after leaving the post of cathedral organ master four years ago after 45 years. The Church settled out of court before the case was heard in an agreement which involved a confidentiality clause preventing parties discussing the case.
Mr Turner said: "I am disturbed by references to 'legal reasons' which would prevent my playing the organ, as the deceased and her family wished.
"It is an undoubted prerogative of the director of music and minister to refuse permission for any reason they like, but I have the assurance of my lawyer that my out-of-court settlement with the Cathedral provides no 'legal reasons' of any kind."
A Kirk spokesman said: "A representative of the Church wrote to a member of the family of Mrs Houston to express sincere sympathy for their loss and to assure him that there was no intention on anyone's part to be unkind or unsympathetic towards the family.
"He highlighted however that there is a legal contract which means Church musicians cannot be forced to waive their right to play at all wedding and funeral services, a clause familiar to Mr Turner.
"The writer also highlighted a legal agreement which prevents the Church and Mr Turner discussing why he is no longer employed by the Church."
The fee for playing had been waived by Mr Turner and the family had planned to donate it to the cathedral.