Waste product generated by special agents (6)
I believe the answer is:
stools
'waste product' is the definition.
(stools are pieces of faeces)
'special agents' is the wordplay.
'special' becomes 's' (common abbreviation as in Special Air Service).
'agents' becomes 'tools' (both can mean things or people used for a purpose).
's'+'tools'='STOOLS'
'generated by' acts as a link.
(Other definitions for stools that I've seen before include "Simple seats, without back or arms" , "Seats without backs or arms" .)