It was announced yesterday that the eight-year-old would miss the rest of the season, including the Queen Mother Champion Chase at Cheltenham that he won last year.
Sprinter Sacre was pulled up at Kempton on December 27 and diagnosed with an irregular heartbeat. Since then, he has not looked the same.
Henderson told BBC Radio 5 Live: "He's such a brilliant horse you can just tell [he isn't right].
"He was working to 90% of his ability and his capacity. Our job is to send him back to the garage, if you like, and get him back and have a full MOT."
Sprinter Sacre has won 14 of the 16 races that he has taken part in and won £724,886 in career earnings.