The forward's future at Manchester United has been the subject of intense speculation after he reportedly told the club he wanted to leave so he can play in the Champions League.
Several reports had also linked him with a potential move to Munich.
The Portuguese, who scored 24 goals in all competitions for United last season as they finished sixth in the league and missed out on Champions League qualification, did not join the squad for the pre-season tour starting in Thailand, citing family issues.
"We discussed this issue because otherwise we would not be doing our job properly," Kahn told Germany's SportBild magazine.
"I personally consider Cristiano Ronaldo one of the greatest footballers ever on this planet."
Seven-time Bundesliga top scorer Robert Lewandowski (33) left the Bavarians earlier this month to join Barcelona.
"But we came to the conclusion that despite all the appreciation for Cristiano, he would not have fit in our philosophy in the current situation," Kahn said.
Bayern, who last season won their 10th straight league title, have already brought in French teenager Mathys Tel, Dutch defender Matthijs de Ligt, striker Sadio Mane as well as Ajax Amsterdam duo Ryan Gravenberch and Noussair Mazrouai.
Ronaldo has also been linked wityh a move back to the Spanish capital, this time with Atletico Madrid. However their President claimed the rumour was fiction, adding that it was "practically impossible" for them to sign Ronaldo.
