Government Waste Corrections Act of 1999

Sets forth agency authorities with respect to audits and activity procured by contract. Authorizes the contractor, as part of a contract, to notify any person of possible overpayments made to such person and identified in the audit and to respond to questions concerning such overpayment. Outlines required contract terms and conditions, including confidentiality requirements and required periodic reports and notifications from the contractor concerning identified overpayments as well as the possibility of fraud or other criminal activity discovered during the audit. Requires the agency head to conduct a cost-comparison process to determine whether to conduct audits and activity in-house or by contract.

Limits the disclosure by non-governmental entities of individually identifiable information obtained through the performance of an audit and activity. Requires such entities to destroy such information upon conclusion of the matter for which the audit or activity was undertaken.

Requires audit and activity amounts recovered to be used for recovery audit costs and a management improvement program established under this Act, with the remainder to be deposited into the Treasury. Provides exceptions.

Directs each agency conducting such audits and activity to conduct a management improvement program which shall address problems contributing to agency overpayments. Allows such program to seek to reduce errors and waste in other agency programs and operations by improving the agency's staff capacity, information technology, and financial management. Requires the Director of the Office of Management and Budget to coordinate and oversee the implementation of this section, including providing guidance for audit standards. Authorizes the Director to: (1) limit the amounts paid to contractors as a recovery fee; and (2) exempt an agency from the audit and activity requirements when compliance would impede the agency's mission or would not be cost-effective (requiring a report to Congress on any such exemption). Requires three annual reports from the Director to the President and specified congressional committees on implementation of this section. Requires the Comptroller General, after each such report, to report to the Director and such committees.

Requires each agency to begin such audit and activity within 18 months after the enactment of this Act.