Elsie Houston, a volunteer guide at Glasgow Cathedral for 30 years, had asked for her late husband Reverend Freddie Houston's music to be played at last Friday's service in the surroundings where she had also enjoyed concerts led by then organist and long-term family friend John Turner.
The family said they were stunned to be told it was not possible for Mr Turner - the cathedral's organ master for about 40 years - to provide the accompaniment because of an old employment dispute with the Church Of Scotland over his former job.
Mrs Houston's daughter, Margaret, said the Reverend Dr Laurence Whitley, who led the service, rejected a personal plea from the family to set aside the dispute "for an hour" to allow Mr Turner to recite the pieces.
The Church said the employment dispute had involved a confidentiality clause and those concerned could not comment about the Houston family funeral arrangements.
A Kirk spokeswoman added that the compilation of Mr Houston's work was played at the service.
Margaret Houston said Mr Turner, who attended the service and gave a reading, was vital to the correct recital of the composition and the family remained saddened despite the efforts from the visiting organist.
She said: "The music had been composed by my father and Mr Turner worked with him. Not just any musician could recite my father's music."
She said she appealed at Presbytery level and to the Kirk's administrative headquarters in Edinburgh before the funeral.
Mrs Houston, who died aged 87, had not been in the cathedral for four years after struggling to recover from a stroke.
She was a "full-time minister's wife and mother" after marrying and moved to Shetland for her husband's first charge. They moved to Townhead Blochairn parish in Glasgow where they stayed from 1959 until 1987 when the clergyman died from leukaemia.
Miss Houston, the youngest of five siblings, one of whom died three years ago, said one of her mother's passions was giving tours of the 817-year-old cathedral to visitors.
She said: "My mother was interested in history and was a guide at the cathedral, showing people round every Thursday and sometimes twice a week.
"It was a place she loved, and she used to go to see concerts by John Turner there before her stroke."
Miss Houston, who lives in London, said: "It would be nice to have an apology, but then again it is more of the fact this has actually happened.
"I want it to be brought to the public's attention in the hope they won't treat people this way again.
"It is so un-Christian."
She added: "My mother was totally selfless. This is the thing that makes it really annoying. She devoted her life to the Church. I felt I had to say something as my mother would have wanted me to."
At the service she read out to mourners: "My mother believed in speaking out for what she felt was right.
"She would have wanted me to tell you we are saddened her request to have music by my father played on the organ today by a family friend was refused in this her place of worship."
Miss Houston also said yesterday: "We as a family do not know anything about these 'legal reasons' but we could not see that there would be a legal reason to stop Mr Turner playing the organ at a private family funeral."
The organist, who left his post in 2010, had been involved in an employment wrangle about the departure before a settlement was reached out of court.
His successor, Iain Simcock, was less than a year into his appointment before being dismissed for alleged misconduct, which he denied.
Richard Pratt, the director of music, and Mr Whitley were contacted but declined to comment, as did Mr Turner.
A Church Of Scotland spokeswoman said: "It is for the director of music to manage the use of musical facilities in the cathedral. In this instance, permission regrettably cannot be granted to this former employee.
"The cathedral was happy for the wishes of the family for a special piece of music, to be met by those who are currently responsible for the music in the cathedral."