Can my employer withhold wages to pay back per diem which they mistakenly determined i qualified to get?

when i was hired i turned in a utility bill for proof of address so they could determine if i qualified for per diem. they determined to give me $30 a day. now the main contractor's auditors have said i did not qualify for per diem and i owe them $1250.00 which they will take from my paycheck, either all at once or i can "agree" to payments taken from my check? If i don't agree, they don't guarantee my job and they will keep my final check. can they do this?