In the Department of Defense authorization legislative signing statement issued on October 5, 1999 by the White House, President Clinton announced that he would not comply with certain sections of the National Defense Authorization Act for Fiscal Year 2000 dealing with nuclear laboratory security:
The most troubling features of the Act involve the reorganization of the nuclear defense functions within the Department of Energy… Particularly objectionable are features of the legislative charter of the new National Nuclear Security Administration (NNSA) that purport to isolate personnel and contractors of the NNSA from outside direction, and limit the Secretary's ability to employ his authorities to direct — both personally and through subordinates of his own choosing -- the activities and personnel of the NNSA. Unaddressed, these deficiencies of the Act would impair effective health and safety oversight and program direction of the Department's nuclear defense complex. Other provisions of S. 1059 have been faulted by the Attorneys General of over 40 States as placing in question the established duty of the Department of Energy's nuclear defense complex to comply with the procedural and substantive requirements of environmental laws. Moreover, the Act removes from the Secretary his direct authority over certain extremely sensitive classified programs specified in the Atomic Energy Act, and establishes in the NNSA separate support functions — such as contracting, personnel, public affairs, and legal — that are redundant with those now within the Department. This redundancy even extends to the counterintelligence office reporting directly to the Secretary that was established in accordance with my Presidential Decision Directive 61, and which was designed to be the single authoritative source of counter-intelligence guidance throughout the Department. The Act establishes a companion counterintelligence entity within the NNSA, compounding simple redundancy with the blurring of lines of authority that can too readily result because the NNSA is largely immunized from outside direction within the Department. Experience teaches that these are not abstract deficiencies. As the Hoover Commission concluded half a century ago, the accountability of a Cabinet Department head is not complete without the legal authority to meet the legal responsibilities for which that person is accountable. The Act's provisions summarized above skew that authority. These provisions blur the clear and unambiguous lines of authority intended by Presidential Decision Directive 61, and impair the Secretary of Energy's ability to assure compliance at all levels within the Department of Energy with instructions he may receive in meeting his national defense responsibilities under the Atomic Energy Act. The responsibilities placed by S. 1059 in the National Nuclear Security Administration potentially are of the most significant breadth, and the extent of the Secretary of Energy's authority with respect to those responsibilities is placed in doubt by various provisions of the Act.
Therefore, by this Statement I direct and state the following: 1. Until further notice, the Secretary of Energy shall perform all duties and functions of the Under Secretary for Nuclear Security. 2. The Secretary is instructed to guide and direct all personnel of the National Nuclear Security Administration by using his authority, to the extent permissible by law, to assign any Departmental officer or employee to a concurrent office within the NNSA. 3. The Secretary is further directed to carry out the foregoing instructions in a manner that assures the Act is not asserted as having altered the environmental compliance requirements, both procedural and substantive, previously imposed by Federal law on all the Department's activities. 4. In carrying out these instructions, the Secretary shall, to the extent permissible under law, mitigate the risks to clear chain of command presented by the Act's establishment of other redundant functions by the NNSA. He shall also carry out these instructions to enable research entities, other than those of the Department's nuclear defense complex that fund research by the weapons laboratories, to continue to govern conduct of the research they have commissioned. 5. I direct the Director of the Office of Personnel Management to work expeditiously with the Secretary of Energy to facilitate any administrative actions that may be necessary to enable the Secretary to carry out the instructions in this Statement. The expansive national security responsibilities now apparently contemplated by the Act for the new Under Secretary for Nuclear Security make selection of a nominee an especially weighty judgment. Legislative action by the Congress to remedy the deficiencies described above and to harmonize the Secretary of Energy's authorities with those of the new Under Secretary that will be in charge of the NNSA will help identify an appropriately qualified nominee. The actions directed in this Statement shall remain in force, to continue until further notice. (Emphasis Added)
As the Wall Street Journal noted, this was not the first time the Clinton administration has failed to follow explicit statutory language. In 1993, Department of Education attorneys instructed officials to ignore the word "shall" in a statute requiring the department to set student loan interest rates at the level charged by private banks. To do so would, in the words of a department lawyer, frustrate the statutory purpose of the direct loan program.
House Armed Services Chairman Floyd Spence sent a letter to President Clinton stating that the signing statement undermined the administration's credibility in handling nuclear secrets and would be met with resistance in Congress. Spence indicated that he would attempt to create a fully autonomous agency at the Department of Energy instead of the semi-autonomous one established in the defense bill.