Former Germany international Sammer has had "a tiny circulatory disorder in the brain," and will not rush back to his duties with the team who are chasing a treble this season.
"There are no limitations for me and the doctors said I will make a full recovery," he said in a club statement. "I will, however, take the necessary time to recover in order then to be at Bayern's disposal with all my strength."
The 48-year-old, who was European Footballer of the Year in 1996, played for and coached Borussia Dortmund and VfB Stuttgart before joining Bayern in 2012, helping the club enjoy great success including a treble-winning 2013 campaign.
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The Bavarians can repeat that feat and need one win in their last three league games to secure a record fourth consecutive Bundesliga title.
They are also through to the German Cup final and face Atletico Madrid in the Champions League semi-finals next week.
"The most important thing is for Matthias Sammer to fully recover," said club CEO Karl-Heinz Rummenigge.
"Matthias knows we will give him all the time he needs to get back to his old strength."
(Reporting by Karolos Grohmann; Editing by Ken Ferris)
