Federal Wages & Hours Law requires that the employee be paid for all hours worked. After that there is a list of allowable deductions for federal,state,local income taxes, voluntary payments for employee benefits,401K/retirement contributions, etc. While the fee for ACH may not be specifically prohibited, it may not be an allowable deduction. It could be construed as not paying the employee for all hours worked. Check your state Wages and Hours Law. It may have similar terms.