The Bundesliga champions moved six points clear at the top of the table with a 3-1 win over Hannover on Saturday but Boateng was concerned by their display in the first half.
Arturo Vidal put Bayern ahead but Hannover levelled through Charlison Benschop after Niclas Fullkrug had missed a penalty. Jupp Heynckes' side did not regain their lead until Kingsley Coman struck with 67 minutes played, before a late Robert Lewandowski penalty made the points safe. Bayern host PSG in their final Champions League group game next week looking to avenge a 3-0 defeat in France, but Boateng fears they will suffer a similar fate if they do not improve upon the display against Hannover.
"We did not defend very well after losing possession and gave Hannover a lot of space, especially in the first half," said the centre-back.
Bayern must win 4-0 at the Allianz Arena to leapfrog PSG and finish top of Group B.