My wife is a salaried employee. She receives 13 days of PTO every 6 months. However, she took 2 days of PTO and they deducted her pay. Her payroll office admits that this was wrong and that they owe her 2 days pay. The problem is this, it has been almost 2 months now since they deducted her pay and she still has not been paid for those 2 days. My question is this, what can she do or who can she contact to help resolve this issue? Are they in violation of anything by not paying her in a timely manner?

There's really not anything she can do to resolve this except work with them internally. No Federal law and no law in any state requires an employer to provide vacation or PTO in the first place. If she is a non-exempt employee, she never has to be paid when she does not work, and if she is an exempt employee, she can legally be docked for taking time off for personal reasons (such as vacation). They are not in violation of any laws and there is no regulatory agency that dictates to the employer when, or if, vacation or PTO must be paid.

United States department of Labor standards for pay deductions says:

Deductions from pay are permissible when an exempt employee: is absent from work for one or more full days for personal reasons other than sickness or disability; or absences of one or more full days due to sickness or disability if the deduction is made in accordance with a bona fide plan, policy or practice of providing compensation for salary lost due to illness; to offset amounts employees receive as jury or witness fees, or for military pay; for penalties imposed in good faith for infractions of safety rules of major significance; or for unpaid disciplinary suspensions of one or more full days imposed in good faith for workplace conduct rule infractions. Also, an employer is not required to pay the full salary in the initial or terminal week of employment, or for weeks in which an exempt employee takes unpaid leave under the Family and Medical Leave Act.

So if I am understanding that right, since they have a "plan, policy or practicice of providing compensation for salary lost due to illness" which is her PTO then they are allowed to deduct her pay but pay her PTO. She is an exempt employee. Also is it legal to charge her PTO when she works a partial day? From what I have read from the Department of Labor's website, the are not supposed to do that either.

OK, now we know she is exempt (which we didn't know before). The employer has already admitted that they should not have docked her salary without substituting PTO time for it. The question is when are they going to pay her those two days and THAT is what has to be worked out internally.

We also know that the absence was due to illness, which we didn't know before.

Perry, everything I told you is correct based on the information you provided. If you don't give complete details, we can't read your mind.

Yes, it is legal to require PTO for partial day increments. The DOL does not care what "bucket" the pay comes out of as long as all pay due is provided.

http://www.dol.gov/elaws/faq/esa/flsa/006.htm