Staff shortages have reached crisis point in some schools despite an increase in teacher training, a union has claimed.
The executive insisted it was on track with recruitment
Scottish Executive figures show a 30% increase in students enrolled on post graduate certificate of education (PGCE) teacher training courses.
Ministers said they would reach a target of 53,000 teachers by 2007.
But the Headteachers' Association of Scotland (HAS) said that was unlikely as almost all subjects had a shortfall.
A survey conducted by HAS found few subjects and few parts of the country had escaped staff problems.
General secretary Bill McGregor said: "What we're now looking at is a general shortage across the country, in almost every subject there are now major difficulties.
"In some parts of the country it's a problem but there are schools in Scotland where staffing shortage is a crisis."
Mr McGregor called for more work on recruiting and retaining teachers, less workload on staff and efforts to make the profession more attractive.
But announcing the latest figures, Education Minister Peter Peacock said hundreds of new teachers were due to join the profession.
Students on PGCE courses this year went up to 2,397, from 1,722 in 2003/4, and Bachelor of Education numbers increased slightly to 3,368.
Mr Peacock said: "Teaching in Scotland is now an attractive and well-rewarded profession.
The minister said more students would fill vacancies
"That, coupled with our comprehensive education reform programme, means we will continue to attract high quality student teachers into training to fill the vacancies we are creating by expanding the number of posts."
The minister said the number of students on full-time postgraduate certificate courses was set to rise further next year and that pupil numbers were set to fall by more than 100,000 in the next 10 years.
A snapshot in February 2004 found that teacher vacancies were higher than in previous years, with 790 posts being advertised.
Of that number, 335 had been vacant for more than three months.
SNP education spokeswoman Fiona Hyslop said the lack of teachers was a "ticking time bomb within our education system".
"With around half of Scotland's current teachers expected to retire within 10 years we need radical action now to prevent disaster in the future," she said.
"The executive's failure to expand teacher numbers in schools quickly enough means that pupils are being deprived of subject choice and face a steady stream of supply teachers.
"As it stands, Peter Peacock is relying on Scotland's falling population to balance the books."
Tory spokesman on public service reform Brian Monteith said the executive had failed to tackle discipline in schools.
"Under such circumstances, the achievements of teachers in our schools must be seen as nothing short of amazing - and we politicians should be humbled by the fact that we don't do more to help," he said.