Playing off of Radiohead’s idea that karma is enforced by actual police, here he is saying that those actual “Karma Police” are corrupt because, apparently he is innocent of any wrong-doing but is being dealt the repercussions of one who has done a lot of wrong-doing. So someone needs to tell internal affairs to report the misuse of power by the “Karma Police”. Here also lies the double-meaning of internal affairs:
1 – a service that investigates crimes of those that investigate crimes.
2 – a reference to thoughts, ideas, and struggles going on inside one’s mind/psyche.