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I suggest you go to a government agency first, like Imran suggested, especially if your complaint is confidential. Your state probably has a Dept. of Labor or Labor Commissioner who'll handle these things for free.

Only then go to HR. Usually HR are the vermin dogs of management. And if management is evil and knows you're raising red flags, they'll retaliate. But if you have a complaint on file with a government enforcement agency, then you're a whistleblower.

My best guess is that management already knows what's going on. You're unit will show an astonishing high amount of "efficiency." and even a cursory glace at your department will show it's because people are working when no one's supposed to be there.

Also, contact your union if you have one.

Edit:
To find legal authority, check your state's labor code under:
Failure to pay wages
Failure to pay overtime
Failure to keep [accurate employee] records