However, the changes are minimal and the pupil/teacher ratio has remained broadly the same with, in Glasgow, one teacher for every 13 pupils.
The figures showed the number of primary one pupils being taught in classes of more than 25 has dropped by almost 97% from 16,845 in 2006 to 503.
Glasgow employed 5069 teachers of the 51,410 across Scotland.
Nationally that represented a drop of 21 teachers.
The government said the condition of Scots schools also showed improvement with fewer pupils being taught in schools in need of repair since the SNP came to power. The proportion of schools in good or satisfactory condition has increased from 61% in April 2007 to 82% in April 2012.
The number of pupils educated in poor or bad condition schools has decreased from 256,794 in April 2007 to 109,692 in April this year.
Education Secretary Michael Russell said: "We want Scotland to be the best place in the world to grow up and our schools are critical to that ambition.
"Real progress is being made. We are delivering for our schools and our schools are delivering for their pupils."
Labour said the figures showed the SNP was guilty of broken promises on education.
Education spokesman Hugh Henry said: "Alex Salmond came to power in 2007 promising to maintain teacher numbers at 54,136. He quickly ditched this and is now trying to blame local councils for the reduction of 3902.
"He has conned both teachers and parents. No wonder so many newly qualified teachers are finding it hard to get a job. The figures show the shocking reality of the SNP's broken promise."