Reports claimed the Bundesliga champion wanted the midfielder to run down his contract and sign for it on a free transfer next summer, but it has claimed that is not the case.
The midfielder has just a year left to go on his contract, resulting in speculation in the Spanish media that he could play out his deal and sign for the Bavarians on a free transfer next summer.
His position at Madrid has become increasingly uncertain following the signing of Toni Kroos from Bayern, but the club's CEO, Karl-Heinz Rummenigge, has denied any interest in the player.
When asked about the rumors surrounding Khedira, he said: "That is a myth."
The 27-year-old joined Madrid in 2010 after impressing in the World Cup that same summer and went on to become one of Jose Mourinho's most trusted lieutenants in the following three seasons.
However, a serious knee injury halted his progress last term, though he did return in time for the Champions League final victory over Atletico Madrid in May.
Khedira then starred for Germany in their victorious World Cup campaign this summer, reportedly sparking interest from a number of clubs, including Bayern and Premier League side Arsenal.