Department of Energy Contractor Employee Equitable Treatment Act of 2006 - Prohibits any funds from being expended to implement, administer, or enforce the guidance of the Department of Energy (DOE) relating to contractor employee pension and medical benefits policy. (DOE will no longer reimburse contractors for new employees' pension and medical costs under defined benefit plans, but will now reimburse only such costs under defined contribution, market-based plans that vary from the average cost of such market-based plans by no more than 5%.) Requires the Secretary of Energy to: (1) withdraw such guidance not later than one day after enactment of this Act; and (2) reinstate eligibility or reimbursement for benefits or reinstate reimbursement for benefits if the Secretary has acted on such guidance.