Jenny Gilruth has threatened to claw back funding from local authorities to stop teacher numbers from falling any further.
The Cabinet Secretary for Education was speaking in Holyrood following the publication of the latest summary statistics for schools in Scotland, showed numbers decreased by 160 full-time equivalents in 2023, to 54,033.
The largest proportional decreases were in East Ayrshire, Glasgow and Moray.
However, the fall was entirely in primary, special and early learning.
The number of secondary teachers increased.
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The Education Secretary said she had been “clear with councils" that if teacher numbers fell, the Scottish Government would "recoup funding which has been given for this purpose.”
Ms Gilruth said: “For the last two years, we have provided local authorities with £145.5 million of annual funding for the purpose of maintaining additional teachers and classroom assistants – this marked the biggest increase to support teacher recruitment since 2007.
"It is therefore disappointing to see that teacher numbers have decreased slightly. I have written to COSLA today to express my disappointment at this decline.
“My officials will be writing directly to those councils that have not maintained teacher numbers in line with the 2022 census to seek further information on the circumstances behind these reductions.
"I have been clear with councils that if teacher numbers were not maintained nationally in line with 2022 census figures, the Scottish Government may withhold or recoup funding which has been given for this purpose, subject to any mitigating circumstances councils may wish to present."
The statistics also revealed a small drop in the overall average class size in primary schools, down to 23.2 from 23.3.
In 2007, the SNP pledged to get class sizes down to 18.
READ MORE: Is attainment really at a 'record high' in Scottish schools?
There was also a slight drop in the number of new teachers securing a post in the year following their probation, down from 71% from 70%. This followed a drop last year from 80% to 70%.
Meanwhile, the attendance rate in 2022/23 was 90.2% which is a decrease from 92.0% in 2020/21 and the lowest rate since comparable figures began in 2003/04.
There were 11,676 exclusions in 2022/23. Though 40% higher than the Covid-19 affected 2020/21 school year, it is still 22% lower than 2018/19.
Scottish Conservative shadow education secretary, Liam Kerr MSP said: “Teachers are the backbone of Scotland’s education system, but after 16 years of SNP neglect it’s no surprise that many are leaving the profession and not being replaced.
“The recent PISA figures exposed the dire situation in many Scottish schools. Standards have fallen, violence has spiralled out of control and teachers are being subjected to horrific verbal and physical abuse. Many understandably feel that the SNP Government has stood by and allowed this to happen.”
EIS General Secretary Andrea Bradley said Scotland's schools needed more teachers "to support education recovery for Scotland’s young people."
"We need many more teachers to reduce class sizes to enhance the learning experience for all, to provide better support for the even greater number of young people with additional learning needs than last year’s data showed, to help overcome the worrying and growing violence challenges in our schools, and to reduce crippling teacher workload and excessive class-contact time in line with existing Scottish Government commitments.”
The union official said the falling numbers should be a "wake-up call to the Scottish Government and local authority employers that graduates are voting with their feet and choosing other careers where terms and conditions are better."
The Scottish Children’s Services Coalition (SCSC) also hit out at a lack of specialist teachers, support staff and resources to support record numbers of children and young people in schools with additional support needs (ASN).
The figures showed the number of ASN pupils reached a record high of 259,036 in 2023, representing 36.7% of the pupil population, effectively a doubling in numbers over the past decade.
A spokesperson for the SCSC said: “While more children and young people are being identified as having ASN, this is against the increasingly challenging backdrop of a lack of specialist teachers, support staff and the resources needed to support them.
“This is having an impact in terms of surging levels of school violence we are witnessing.”
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