Bayern said on their website that a routine pre-season exam had shown that Robben had a torn muscle in his left thigh, adding he had suffered the injury shortly before the World Cup.
The 26-year-old missed the his team's first two group matches at the World Cup, but then played in the remaining five and helped the Dutch reach the final where they lost 1-0 to Spain after extra-time.
"This is a severe injury," club doctor Hans-Wilhelm Mueller-Wohlfahrt told the club's website.
"I find it irresponsible that this injury has not been precisely diagnosed and that they have let Arjen play.
"For my part, I offered to help with the diagnosis but this was not taken into account."
Robben, who scored two goals at the World Cup but missed a superb chance to put the Dutch ahead in the final, was quoted as saying: "It's a shock for me to get a diagnosis like this on my return.
"I'm very disappointed, this absence is bitter for me and for the team."
"Naturally, Bayern Munich are angry," he said. "Once again, we as a club must pay the bill after a player has been severely injured with his national team."
He scored twice on his debut and went on to help Louis van Gaal's team win a Bundesliga and German Cup double.
