The 26-year-old Australian suffered significant ligament damage and fractures to his right ankle in a big crash during qualifying for last weekend's race at Indianapolis.
The Honda rider bravely opted to race in the US event despite the pain and finished fourth with the help of painkillers and his ankle strapped up - and with surgery to the injury still having not been ruled out.
But Stoner admitted that he is concerned by the high-speed sweeping nature of Brno, as opposed to Indianapolis's predominantly left-handed lay-out, and how it might impact on his ability to ride at pace on the Czech track.
"I'm not feeling too optimistic for Brno after a tough weekend in Indy," he said in a statement from the HRC team.
"The crash in qualifying last week has left me with a serious problem in my ankle and we were fortunate that Indy was a left-hand circuit, so a lot of the weight was off it but we still had changes of direction which hurt a lot.
"In Brno there are many changes in direction and a lot of right hand corners so there will be a lot of weight on my ankle and it's going to be very difficult.
"It's a shame as Brno is a circuit that I usually enjoy due to it's fast and flowing nature, so I'll be resting as much as possible this week and wait to see how we feel when we get on track on Friday."
Honda confirmed that Stoner's medical team is awaiting the results of an MRI scan before deciding whether to operate on his damaged ankle.