The Brazilian Football Confederation (CBF) said that, under the FIFA rules, the players have to be available for training 14 days before the Confederations Cup which starts on June 15.
"This is a constant battle, with each side standing up for their interests," technical director Carlos Alberto Parreira told reporters.
"Bayern sent us a polite letter asking that the player be released (by Brazil to play in the Cup final) and we politely responded that we are not making any exceptions.
"The players are duty-bound to report. We're not picking a fight, it's a matter of obeying the rules."
Club-versus-country battles used to be a constant problem but have been reduced since the introduction of a co-ordinated international calendar, drawn up by FIFA after consultation with clubs and national associations.
Parreira added there had been an exchange of emails and that FIFA had ruled in Brazil's favour.
Brazil face Japan, Italy and Mexico in their Confederations Cup group, with a first match against Japan on June 15 in Brasilia.
There was no immediate comment from Bayern who will be attempting to complete a treble after also winning the Bundesliga and Champions League.
- Sports & Recreation
- Carlos Alberto Parreira