Whistleblower Empowerment, Security, and Taxpayer Protection Act of 2006

Whistleblower Empowerment, Security, and Taxpayer Protection Act of 2006 - Modifies federal criminal law provisions relating to tampering with or retaliating against a witness, victim, or an informant.

Allows a victim of a prohibited personnel practice to bring a civil action against a covered entity and to recover damages. Makes any prospective waiver of the right of any individual to file a civil action under this Act void and unenforceable.

Amends the Inspector General Act of 1978 to allow an Inspector General (IG) to be removed from office prior to the expiration of that IG's term only on one of the following grounds: (1) permanent incapacity; (2) inefficiency; (3) neglect of duty; (4) malfeasance; or (5) conviction of a felony or conduct involving moral turpitude.

Establishes the term of office of an IG as seven years and permits reappointment.

Authorizes an IG to annually transmit an appropriation estimate and request to the Director of the Office of Management and Budget (OMB) and to the appropriate congressional committees, in addition to the head of the establishment concerned. Requires the President to include in each annual budget specified IG appropriation information.

Prohibits any funds appropriated for activities under the supervision of an IG from being reprogrammed, transferred, or otherwise spent for any other purpose without such IG's written consent.

Directs each IG to: (1) create and maintain a hotline for employees confidentially reporting alleged violations; and (2) compile a statistical summary of all allegations for annual reporting to Congress.

Sets forth a special rule regarding revocation of security clearances.

Permits the creation of whistleblower affairs directorates within offices of IGs.

Includes coverage of certain planned disclosures of information under prohibited personnel practices provisions.

Permits petitions for the appointment of special prosecutor to handle cases alleging prohibited personnel practices.

Directs the Comptroller General to study the costs of retaliation against or suppression of whistleblowers.