Los Blancos released a statement on Tuesday claiming that the midfielder had picked up the injury while on international duty.
However, Bierhoff has now hit back, alleging that Madrid knew about the muscle issue before releasing the player to link up with the world champions.
“The player already had problem when he travelled to Germany," the 46-year-old former striker told Bild.
"And what’s more, he had already been examined by doctors in Madrid. They didn’t consider it to be a serious injury!
"After that, Khedira decided to consult a reliable doctor here [and he] diagnosed a muscle tear."
Khedira, who helped Germany win this summer's World Cup, is now expected to be out of action for between six and eight weeks.