"His health problems are more serious than he expected," Czech Davis Cup captain Jaroslav Navratil said in a statement posted Thursday on the website of the country's tennis federation.
No. 25 Stepanek was seeded 22nd for Wimbledon, which begins Monday.
Stepanek was injured in Prague this week while he was preparing for Wimbledon, Czech Davis Cup team spokesman Karel Tejkal said.
Stepanek said in March that he was suffering from a fatigue syndrome and needed at least two months' rest. He returned to action at a challenger tournament in Prostejov this month.
But he pulled out of last week's Gerry Weber Open, the grass-court tournament in Halle, Germany, because of throat inflammation.
Stepanek opened the season by reaching the final of the Brisbane International in January. He lost in the first round of the Australian Open and failed to get beyond the second round in any other tournament this year.