He fell heavily in the Ace Radio Maiden Hurdle at Warrnambool in what was only his second jumps start.
Two other horses fell at the meeting, but neither was seriously hurt.
Anti-jumps campaigners are continuing their push to have the sport banned.
Napthine told reporters that jumps racing had an important place in the history of racing and the state's heritage, and was important for jobs in the racing industry.
He urged opponents to give jumps racing an opportunity to improve its safety record.