Mr Kneen received £200,000 in salary and £12,000 of benefits plus another £14,000 in pension contributions to take his remuneration for the year to £226,000.
This is a drop of £70,000 or 23.6% from the £296,000 he received in 2012.
IndigoVision saw its annual pre-tax earnings fall 12.7% to £2.08 million and had to issue a profit warning in the course of the year to July 31.
Profit margins have been under pressure as IndigoVision's product mix has shifted from encoders, where prices are falling, to intelligent cameras.
The company is now entering the final year of a three-year turnaround plan launched after the controversial exit of Mr Kneen's predecessor Oliver Vellacott. This has included putting greater emphasis on the release of new products - including 13 camera models in the last financial year.
Increased spending on research has supported the development of products including explosion proof cameras for the oil and gas industry, and 20 megapixel cameras to service stadiums and casinos.
Mr Kneen joined IndigoVision in 2003 and has run the company since late 2011 after IndigoVision had a messy split from his predecessor and company founder Mr Vellacott, who made several buy-out offers and sought to oust chairman Hamish Grossart from the board.
Earlier this month, Mr Kneen picked up 25,000 shares under an options scheme.