The ex-Germany coach was not impressed with the Bavarians' victory against Borussia Monchengladbach on Friday, but hailed Mario Gotze as an "exceptional" player
Die Roten beat Gladbach 3-1 on Friday thanks to goals by Arjen Robben, Mario Mandzukic and David Alaba.
However, Beckenbauer was not impressed with the victory, saying his former side needed to tighten up at the back as there were too many spaces for their opponents to exploit.
"I was surprised at how Bayern struggled," the 67-year-old told Sky.
"During the pre-season matches, they played flawlessly, except for the [DFL Supercup defeat] against Borussia Dortmund.
"On Friday, however, they played normally again.
"I'm curious as to how quickly they will be able to implement Guardiola's philosophy and which players will prevail in the end.
"Shifting between offence and defence can still be improved. It's important that Guardiola makes the team more compact."
The 1990 World Cup winner went on to praise €37 million signing Mario Gotze, who scored twice during Bayern's 4-1 friendly win against Gyor on Sunday.
"He shares exactly the same philosophy that Pep expects from the team," he added.
"He's exceptional with everything that happens on the ground. However, his team-mates should avoid providing him with high balls."