Dani Pedrosa said he feared he had broken his foot when he was struck by debris in Friday morning MotoGP practice at Brno.
The Honda rider was left limping after being hit by a rock thrown up when Valentino Rossi went off-course.
Pedrosa went on to set the fastest time in both practice sessions.
"I was pretty lucky with the incident this morning as it could have been a lot worse," he said. "There were two massive rocks that flew up, one hit my left foot hard and the other one hit my screen and chin.
"At the beginning I thought I had broken something in my foot but fortunately it's OK, just a lot of swelling. Anyway the pain is going down from this morning so that's a good thing."
Pedrosa is already the only works Honda rider in the field due to his team-mate Casey Stoner leaving the Czech Republic to have surgery on the ankle he injured in qualifying for last weekend's Indianapolis Grand Prix.
Despite being quickest on Friday, Pedrosa said Honda still had things to fine-tune before qualifying.
"Today we spent time working on the tyres and set up of the bike," said the Spaniard, who closed to within 18 points of championship leader Jorge Lorenzo by winning at Indianapolis last Sunday.
"We were trying to get the maximum time on the track as tomorrow we don't know how the weather will be so it was important to have a lot of time in the dry.
"The feelings were improving but we still have some work to do especially with electronics and suspension."