Hayden was knocked unconscious and fractured his right hand when he had a violent high-side during Saturday's qualifying session. He was not given clearance to race.
The Brno race takes place just seven days after Indianapolis, and Ducati team boss Vito Guareschi said Hayden's hand injury was a concern.
"Over the next couple of days, we'll know whether or not Nicky will be able to be there," said Guareschi. "He has two small fractures in his right hand, so he'll undergo some additional exams to check whether it will be possible to ride or if it's better to skip the Czech Republic and recover for Misano."
Ducati will take Hayden's bikes to Brno ready to use as normal if he is given medical clearance.
The American felt he could have raced at Indianapolis, but respected the doctors' decision.
"I realise that I had a pretty big one yesterday and was knocked out for quite a while, so to be here today more or less OK is positive," said Hayden. "There's no really big damage, although injuries to the right hand are always worse than the left.
"Even if I thought I could have ridden today, the doctors wouldn't have cleared me because I was knocked out for so long. Concussions need to be taken seriously, so I don't fault them for that."