The club said discussions would take place at the Allianz Arena on July 2 involving 10 supporters' representatives, members of the board, players and club employees.
"Our aim is to have a harmonious, successful, tolerant and respectful Bayern Munich," CEO Karl-Heinz Rummenigge told the club's website.
The club were stunned and angered when fans protested against president Uli Hoeness and plans to sign goalkeeper Manuel Neuer from Schalke 04, one of Bayern's bitterest rivals.
Despite "No Neuer" signs being displayed at matches, the goalkeeper joined Bayern last week and the club hope he will become as influential as Oliver Kahn.
"The aim of the round table is to talk about the relationship between the club and its fans in an open exchange to reach an agreement over a future togetherness," said Bayern.
Bayern said it had 2,900 registered fan clubs with more than 200,000 members.
The team finished a disappointing third in the Bundesliga last season and must play-off over two legs for a place in next season's Champions League.
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