Teachers in the city have said the lack of supply staff is causing serious concern and that the issue is having a negative effect on learning in schools.
The EIS union says members are reporting "exacerbating stress levels among teachers and managers across the city" and the union has warned the problem is "impacting on attainment and exam preparation".
Hugh Donnelly, Glasgow Local Association Secretary for the EIS, Scotland's largest teaching union, said: "Our members, including heads and deputes, are making significant efforts to cope with the shortage of supply cover.
"Significant time and effort is being spent on trying to secure supply teachers and rearranging timetables in order that pupils are provided with some cover.
"We are in constant dialogue with Glasgow City Council.
"Efforts are being made to improve the availability of supply teachers but there remain significant problems in primaries and certain secondary subjects. Recently, a joint national survey identified serious concerns with short-term supply.
"There is little doubt there is a link between short-term supply problems and pay and conditions, and the impact of the reduced rates for short-term supply teaching."
The union says teachers are making significant efforts to cope with the situation but says teachers and managers are struggling to meet the needs of young people in Glasgow's schools.
It claims teachers and managers are co-operating and being flexible, often at very short notice, but the situation is the worst the union has seen for a number of years. The EIS is now calling for local and national action to resolve the problem.
In a statement, the union pointed to an example of a class having been taught by 29 teachers this session because of a subject shortage and says another school was three biology teachers short at one point.
In primary schools, head teachers and deputes are covering classes leading to increased workload and pressures, it said.
The statement added: "The problem is not confined to Glasgow. It is clear this is an issue of national significance.
"One of the main concerns is the plight of those pupils who will be sitting their Standard Grades and Highers in a few months against a background of significant curricular change. This is putting significant pressure on schools.
"Ironically, this comes at a time of significant improvement in teacher absence."
Mr Donnelly added: "We need to look at the impact in the reduction of the short-term supply rate, the training and recruitment of teachers nationally, and ways to engage those retired teachers who would normally be available to take up the slack of short-term absence.
"Of course, we need to improve the prospects of new and recently qualified teachers who are expected initially to put up with occasional and unpredictable supply work which leads to many being lost to the profession, going into other jobs or elsewhere to find employment."
A spokesman for Glasgow City Council said: "We share the concerns of the EIS about the shortage of supply teachers. This is a national issue and Glasgow has been affected equally with other local authorities."
A Scottish Government spokesman said: "The employment of teachers, including supply teachers, is a matter for the local authorities.
"The Scottish Negotiating Committee for Teachers is currently monitoring supply issues and we will play our part in those discussions.
"The numbers of teachers trained each year includes an allowance to ensure there is a pool of supply teachers from which schools can draw as necessary."