Hayden was ruled out of the Indy MotoGP race when he fractured his right hand and was briefly knocked unconscious in one of several large accidents last Saturday.
Although he said he felt capable of riding at Brno, Hayden admitted it would be unwise.
"It's tough to miss another race. I don't have big problems, but my hand is still very swollen and I don't have much strength, and of course right-hand injuries are worse for motorcycle racers," he said.
"I would have been at far less than 100 per cent, and if I used too much force or crashed again, I could displace the breaks and possibly be in big trouble. Obviously, the head is even more important, and with the amount of time I was unconscious, I'm still dealing with a headache.
"The main thing is all the doctors told me racing was a really bad idea and not smart, and everybody on my team agreed. As much as the racer in me doesn't like staying at home and missing track time and points, I need to listen to the experts and try to heal up and get ready for Misano.
"That's an important race for me and for Ducati, and I'll be doing all the rehab to come back as fit as possible. I don't like it, but it's the right thing to do."
Ducati will not field a replacement rider, with Valentino Rossi representing the factory team alone in the Czech Republic.