The Portugal international freely admits the Champions League holders "look very good" but he says that they leave too much space in behind their back four
The Bavarians are being tipped by many pundits to become the first side to retain the Champions League, having already eased into the quarter-finals with a 3-1 aggregate win over Arsenal on Tuesday night.
However, while Pepe has been impressed with the way in which Bayern have managed to progress under new boss Pep Guardiola this season, he feels that the reigning European champions are far from flawless.
“Bayern work very hard, but they also leave a lot of space over the defenders’ shoulders," the Portugal international told Onda Cero.
"They’re a team that is doing its job very well and they’re still developing. They’re still not a complete side but they look very good."
Meanwhile, Pepe challenged the perception some people have of his team-mate at club and international level Cristiano Ronaldo, claiming that it is unfair that the Ballon d'Or holder is sometimes portrayed as arrogant and aloof.
“A lot of people have the impression that he’s cocky and unfriendly, but he’s a normal guy," Pepe insisted.
"[He's] very close to his friends and he’s a person who works really hard to reach his goals.
"When he doesn’t manage that, he gets very angry. He closes himself up in his world to be able to change that and improve.
"He wants to be the best and better himself. He’s a really complete player.”
Pepe also argued that the way in which Ronaldo is mentoring Madrid starlet Jese proves what a class act the star is on and off the field.
“Cristiano talks to Jese a lot," he explained. "He knows that he’s the mirror Jese looks at himself in.
"Jese watches him a lot, he asks him a lot of questions and Cristiano is always looking out for him.”