HHS Employee Compensation Reform Act of 2012 - Amends the Public Health Service Act to state that provisions authorizing the appointment of special consultants or authorizing individual scientists to receive fellowships do not authorize the designation, appointment, or employment of any special consultant, fellow, or other employee by an agency outside of the Department of Health and Human Services (HHS).
Prohibits more than 5% of the total number of HHS employees from serving as special consultants or fellowship recipients. Limits, with exceptions determined by the HHS Secretary, the compensation payable to such an individual for a 12-month period to 150% of the annual rate payable under level 1 of the Executive Schedule, prorated for shorter periods.
Requires an annual report to Congress concerning the employment of such individuals.