Nikonorov, who joined British Canoeing 16 years ago from Russia, guided Ed McKeever to K1 200m gold at London 2012 - a title retained for Team GB by Liam Heath four years later in Rio - while Heath and Jon Schofield also won K2 200m in South America.
He also coached the trio to a host of World Cup, European and World Championship medals, en route to establishing Great Britain as one of the 200m racing powerhouses.
Technical coach Miklos Simon has also recently left the sprint programme in order to return to his native Hungary, after ten years working with British athletes - most recently, those on the women's Olympic programme.
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"Alex has been a fantastic asset for British Canoeing and has made a major contribution to the success of the canoe sprint programme, which is unrivalled in 200m racing worldwide," said John Anderson MBE, British Canoeing performance director.
"Whilst I am disappointed that he has decided to move on, I fully respect his desire for a new challenge in the build-up to Tokyo 2020.
"On behalf of British Canoeing I would like to thank him for all his incredible work with our programme and wish him all the very best for the future."
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Canoe Sprint Men's Canoe Single 1000m Quarterfinal - Tokyo 2020 - Olympic Highlights