Bayern also announced that 36-year-old goalkeeper Jorg Butt will extend his contract with the club, who are widely reported to be chasing Schalke 04's Manuel Neuer, for another year.
"Thomas Kraft's understandable goal is to be the number one," sporting director Christian Nerlinger told the club's website.
"That is something we cannot guarantee him."
Butt has regained his place in the first team under interim coach Andries Jonker following Van Gaal's dismissal three weeks ago.
Van Gaal had replaced Butt with 22-year-old Kraft at the start of the year and refused to reverse the decision despite concerns voiced by the club's various high-profile leaders.
Former goalkeeper Oliver Kahn was another who questioned the wisdom of Van Gaal's choice.
"Van Gaal did not take our advice. It has caused great unease in the whole defence," club president Uli Hoeness after the Dutchman was fired.
Van Gaal, on the other hand, singled out Kraft for praise after his performance in their 1-0 win away to Inter Milan in the first leg of their last 16 Champions League tie.
Bayern chairman Karl-Heinz Rummenigge said Jupp Heynckes, who takes over as coach next season, had wanted Butt to say on.
"Jorg Butt is a first-class goalkeeper," said Rummenigge. "I'm very happy that he's staying here for another year."
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