The world champion crashed his Ducati on the final day of night testing at the track at the left-handed turn two.
And, despite the 22-year-old Australian emerging unhurt, he demanded that the Motorcycle Safety Commission take immediate action in reducing the size of the stones in the gravel trap ahead of the race.
"I had a crash going into turn two, but luckily I wasn't seriously hurt," said Stoner.
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"Having said that I think that in the Safety Commission we need to talk about the size of the gravel pieces because here, like at Jerez, they're too big - they're more like rocks than stones and they can hurt you even in a small crash."
Stoner has been a big advocate of safety over the past 12 months. He insisted that re-surfacing work at Donington Park had made the track surface dangerous to the point that it was "like driving on ice."
And he also branded the revisions to the legendary Assen circuit as "hugely disappointing" last summer as well as calling the re-surfacing of Laguna Seca "slippery beyond belief."
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