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Kiyonari, who was unbeaten this season, escaped serious injury in the crash on lap six of race one at Mallory Park.

His HM Plant Honda team-mate Rutter held off Hawk Kawasaki's Glen Richards and Ducati's Leon Haslam to win.

Rutter again got the better of Richards in race two to take over at the top of the championship standings.

Rutter now leads Kiyonari by 119 points to 100, with Gregorio Lavilla third on 88.

Lavilla recovered from a fall in the first race to take third place in race two.

Kiyonari now faces a race against time to be fit for the next round at Oulton Park.

"I was pushing him hard, hoping he might make a mistake, but not for that to happen," said Rutter.

"I've never known so many stoppages but we still got some decent races in and I just had that little bit more speed than Glen."

Race one results:
1 Michael Rutter (Honda) 21mins 48.024secs
2 Glen Richards (Kawasaki) at 6.706secs
3 Leon Haslam (Ducati) at 10.354
4 Sean Emmett (Yamaha) at 11.299
5 Scott Smart (Suzuki) at 13.465
6 Dean Thomas (Kawasaki) at 17.638
7 Michael Laverty (Honda) at 18.015
8 Gary Mason (Honda) at 21.170
9 Danny Beaumont (Honda) at 23.640
10 Steve Brogan (Honda) at 30.548
11 John McGuinness (Yamaha) at 30.803
12 Dennis Hobbs (Yamaha) at 31.240
13 Tristan Palmer (Kawasaki) at 33.631
14 Jonathan Rea (Honda) at 33.896
15 James Buckingham (Suzuki) at 34.249