More than half a million of those lost days are as a result of suspensions, which last between three and five days on average, with some involving children as young as four.
The figures, from The Children's Society, show that exclusions are rising fastest in primary schools. Overall, there were 137,000 temporary exclusions in 1996-97, and more than 12,200 were permanently excluded.
The organisation has blamed league tables and inspections for the increase as schools try to improve their exam results and their public image by getting rid of unruly youngsters.
The study, called No Lessons Learned, also showed huge variations in exclusion figures across the country and between different schools.
One local authority recorded 24 times as many temporary exclusions as another of similar size, while one secondary school recorded 469 exclusions over the year - an average of two per school day.
The study found that a fifth of local authorities did not keep information on temporary exclusions, while four out of 10 had no record of the number of days that suspensions lasted.
There was also little, if any, analysis of exclusions among ethnic-minority pupils. Research shows that African-Caribbean boys are four times more likely to be excluded than other pupils.
Ian Sparks, chief executive of The Children's Society, said: "Exclusions carry heavy penalties for us all.
"They damage children's education and their future, while parents are left having to drop everything, including their work, at short notice.
"Society also pays for exclusions through the high costs of alternative education programmes and increased crime as disaffected children drift from school out onto the streets."
He added that the study had thrown up some "disturbing" findings about the way local authorities dealt with exclusions.
"Without basic information, local authorities won't be able to put into place the policies needed to help teachers and parents tackle children's behaviour problems and get them back into the classrooms," Mr Sparks said.
The society recommended offering more training and support to teachers who have to deal with difficult behaviour from pupils.
It also wants case conferences to be held with pupils threatened with exclusion, their parents, teachers and local authorities so that a reintegration plan can be worked out.