Department of Veterans Affairs Employment Reduction Assistance Act of 1999

Department of Veterans Affairs Employment Reduction Assistance Act of 1999 - Directs the Secretary of Veterans Affairs, before obligating any resources for voluntary separation incentive payments (payments), to submit to the Director of the Office of Management and Budget a strategic plan outlining the use of such payments and a proposed organizational chart for the Department of Veterans Affairs once such payments have been completed. Requires such plan to include: (1) the positions and functions to be reduced or eliminated; (2) their effects on meeting efficiency, budget, or staffing goals; (3) the period of time during which such incentives may be paid; and (4) a description of how the affected Department components will operate without the eliminated functions and positions.

Authorizes the Secretary to make such a payment only to reduce or eliminate positions or functions identified in the plan. Requires such payments to be in a lump sum and no greater than $25,000 apiece. Requires full repayment from any individual who is subsequently reemployed with any Federal department or agency, with exceptions for certain employment in which the individual possesses unique abilities and is the only qualified applicant available.

Requires the Department to remit to the Office of Personnel Management for credit to the Civil Service Retirement and Disability Fund 15 percent of the final basic pay of each individual receiving such payments.

Reduces the total number of full-time equivalent employees in the Department by one for each individual receiving such a payment. Authorizes the President to waive such reductions upon a determination of the existence of: (1) a state of war or other national emergency; or (2) an extraordinary emergency which threatens life, health, safety, property, or the environment.

Provides for continued temporary health insurance coverage for individuals receiving such payments.

Prohibits any payment based on the separation of an employee after September 30, 2004.