The EIS trade union has spoken up about the "unjust and unacceptable" situation, as it noted that 27 of Scotland’s councils have some form of charging fee in place for families.
This can include schools asking parents to pay tuition fees for music lessons, instrument hire charges or a combination of both.
Only five local authority areas offer free music lessons.
The union said a rise in charges was "even more worrying" as in some parts of Scotland the annual cost of school music lessons can top £300, with charges reaching £524 for one year in one local authority.
In areas where no charges are imposed, the number of pupils studying music has increased by almost a third (31.4%) since 2012-13, it said.
However, this contrasted this with authorities charging as there has been a 12.7% fall in the number of music students over the same period.
Larry Flanagan, EIS general secretary said: "Scotland is rapidly moving towards a scenario where only children from well-off families can learn to play an instrument. This is unjust and unacceptable.
"We must reverse the trend of charging to allow free access to music education for all, particularly those for whom the poverty-related attainment gap has widened as a result of Covid-19."
The Scottish Government is currently investing £25 million to address digital exclusion in schools.
A Scottish Government spokeswoman said: "Music education is of enormous benefit to young people and we are committed to working collaboratively to find solutions to help ensure instrumental music remains accessible to all.
"Local authorities are responsible for ensuring all children and young people have access to the full curriculum, including the expressive arts, and councils should consider the benefits that learning a musical instrument can have on wellbeing and on attainment.
"We know that Covid-19 has brought additional challenges for music tuition in schools."
“Education Scotland has worked with teachers across the country to collect and share emerging practical examples of how teachers are managing music learning under Covid-19.
"Creative ideas include the use of music technology apps on smartphones, running online masterclasses with professional musicians, and using technological solutions to facilitate rich and rewarding physically distanced lessons.”