"Eileen Prior, the organisation's executive director, wants an urgent overhaul of the way teacher numbers are monitored and recruited.
She said: "As it stands we are dealing with a situation where local authorities are finding it difficult to recruit teachers and school leaders, both on supply and permanent contracts.
"From our perspective it appears there is something fundamentally dysfunctional in our manpower planning system.
"We continue to be in a situation about which SPTC is concerned, simply because of the impact on the learning of young people in our classrooms, on the effective running of schools and on the efficacy of the local authority service."
The SPTC represents almost 2,000 parent councils and parent teacher associations across the country and the Educational Institute of Scotland, the country's largest teaching union, echoed the warnings.
A spokesman said: "The lack of availability of supply cover is an issue for schools across Scotland, and is particularly acute in some subject areas and in certain areas of the country.
"This lack of supply cover increases workload pressure on teachers when colleagues are ill, and can have a negative impact on the learning experience of pupils."