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U.S. Dept. of Health and Human Services is required to investigate all complaints. The chances that this will go anywhere after three years is practically nil, because there's no evidence.
Your employer can terminate you, regardless of whether or not the charges are true. In fact, the employer can terminate you for no reason whatsoever. All you can do is exactly what you have done, which is deny the charges, and then wait to see what DHHS decides.
Hope this helps.
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Is evidence required to make such a charge?
A: The only evidence required is (45 CFR 160.306(b)(2)), "A complaint must name the person that is the subject of the complaint and describe the acts or omissions believed to be in violation...."
Is there a statute of limitations on such complaints?
A: 180 days unless waived by DHHS (so, obviously there was a waiver).
I am a federal employee. Can I still be terminated without cause?
A: No. You must be permitted the entire grievance process applicable to your agency. Typically, the Office of Personnel Management procedures are applicable.
This is still an investigation. If you are actually charged with something, then you can ask to have the case dismissed as beyond the statute of limitations.
Re hiring an attorney, once again, you haven't been charged with anything. However, I don't want to disuade you from contacting a lawyer, if that would make you feel more comfortable.
For an employment rights attorney referral, see: http://www.abanet.org/legalservices/lris/directory/main.cfm?id=AZ and www.martindale.com.