David Johnston, convenor of the Scottish Schools Pipe Band Championships, said many classically trained state school music heads "look down" on the bagpipes and pipe band drumming and refuse to offer free tuition.
As a result, fewer youngsters are mastering the instruments and the pipe band tradition could eventually die out, he warned.
Mr Johnston said that 60 schools have signed up for the competition next year, leaving 2600 that are not taking part.
He said: "Quite simply, many classically-trained school heads of music look down on the pipes and want nothing to do with them.
"This means that hundreds of young people desperate to learn pipes and drums in our schools are being denied that opportunity.
"If this worrying trend continues we won't have future pipers and drummers so hearing the roar of pipes and drums on New Year's Eve could become a thing of the past."
In Prestonpans, East Lothian, a group of parents and piping enthusiasts took matters into their own hands five years ago and started a teaching programme at Preston Lodge High School and its neighbouring primaries.