Information on the number of permanent and fixed period exclusions (not pupils) is published at:
1999/2000 http://www.dcsf.gov.uk/rsgateway/DB/SBU/b000298/ index.shtml
Data on permanent exclusions are available for the full period requested.
Data on fixed period exclusions were collected for the first time in 2003/04 via the Termly Exclusions Survey. Since 2005/06 collection has been via the School Census, but in that first year was for secondary schools only. In 2006/07, collection was extended to primary and special schools.
The School Census includes non-maintained special schools, city technology colleges and academies whereas the Termly Exclusions Survey excludes them. This difference in scope and the change in collection mechanism mean that caution is needed when comparing results since 2005/06 with those prior to that.