The cost – for a group lesson – is higher than the price of a private lesson outside of the local authority system.
It is believed that around 150 out of 350 families have written to the council to say they will no longer learn an instrument at school since the fee rise was confirmed at the end of last week.
This comes days after West Lothian became the latest council to introduce fees, scrapping plans to stop percussion and strings tuition in place of charges.
A total of 23 councils now bill parents for musical instrument lessons, with annual prices currently ranging from £117 in Inverclyde to £318 in the Highlands, while a few charge a fee for the annual hire of instruments.
A source told Scotland on Sunday that the council had been “inundated” with letters from angry parents who feel they can no longer afford to keep their children’s tuition going.
“The council has had well over 100 replies, all withdrawing their children from lessons,” said the source.
“It is a very steep fee increase and out of order.
“It’ll decimate the service introducing fees with such severity.”
Teachers employed by the council are responsible for running orchestras, bands and other ensembles, which parents and teachers fear may be scrapped if school-based lessons do not continue.
John Wallace, the chair of the Scottish Government’s Music Education Partnership Group and the former head of the Royal Conservatoire of Scotland, also warned that long-existing ensembles could disappear.
He said: “I feel very sad about Clackmannanshire when I’ve experienced all the great musicians that have come from that neck of the woods over the years.
“No more young people following in the footsteps of role models like Tracy Redfern into the BBC Philharmonic. And large slices of local culture like the Clackmannan and District Band will disappear. No more young players.
“Silence is definitely not golden.”
Clackmannanshire Council said it was still in the process of collecting and collating parents’ letters.
A spokeswoman said: “The Council’s budget seeks to protect essential services while improving our financial sustainability. The concessionary rate remains unchanged and the SQA element of music tuition remains fully funded by the Council.”