The former Germany international feels that the reigning Bundesliga champions are the country's top team at this point
The Bavarians were beaten to the Bundesliga title by BVB in the past two seasons, and Effenberg feels that it was necessary to make changes to the Bayern set-up.
The German giants recently parted company with sporting director Christian Nerlinger and named Matthias Sammer as his replacement.
"Bayern Munich have to make up something. One could even say that Borussia Dortmund have overtaken them," Effenberg was quoted as saying by Sport Bild.
"You can't always point fingers at the players, but you have to look at the staff as well. And that's exactly where Bayern have taken measures. I believe in discussing controversial topics to find solutions.
"Having the occasional argument is part of the job. Internally, within the team, but within the club itself as well. A season like last term where they ended up being runners-up in every competition drives the big chiefs crazy."
Bayern start the 2012-13 Bundesliga campaign with an away match against Greuther Furth on August 24.