This is why specific advice should be sought because other issues are being flagged up. The OP is a sub-contractor and therefore it is possible that the main contractor should only have any certification. Unless the law requires certification of some sort, the main contractor has paid the sub-contractor previously without a problem and it does appear that this was not an issue until now.
CIS is "Construction Industry Scheme" - not sure how this relates to CCTV in Schools. As far as I know the CIS relates to those who are sub-contractors and the main contractor pays the tax/NI.
http://www.hmrc.gov.uk/cis/section2.htm
If there is any breach it is likely the main contractor is the cause of the breach and thus liable. Further investigation required to ascertain who is liable and for what. This cannot be established on a forum