The reorganization was included in a widely popular $288.9 billion defense bill that includes a military pay raise and a 4.4 percent across-the-board increase in Pentagon spending, including more money for military housing and hardware.
The Senate approved the defense measure 93-5, following House approval of the bill last week by a likewise veto-proof 375-45 vote. The administration has indicated a possible veto because of concerns about the nuclear weapons agency, but lawmakers said a veto would be politically difficult given the defense bill's overwhelming bipartisan support.
While some Democrats voiced concern about the new weapons agency within the Energy Department, they said the defense measure was too important to have it sidetracked on the reorganization issue.
Although the new agency will not be totally independent, the legislation insulates the department's nuclear weapons programs and consolidate authority over the government's three nuclear weapons labs.
The reorganization marks the most far reaching fallout yet to months of controversy about lax security at the Energy Department and the alleged theft by China of nuclear warhead secrets from U.S. weapons labs, dating back 20 years.
Supporters of the measure say the new National Nuclear Security Administration within the department would streamline control over nuclear weapons programs and provide increased accountability for security and counterintelligence efforts.
While supporting some reorganization, Energy Secretary Bill Richardson expressed strong reservations about the proposal as it moved through Congress. He argued the new agency would be given too much autonomy and would interfere in security and counterintelligence improvements he already has made in response to Chinese espionage concerns.
Richardson has said he likely would recommend that President Clinton veto the legislation. There was no immediate reaction to the Senate vote from the administration.
"The president would be crazy to veto it," said Sen. Jon Kyl, R-Ariz., who said he was confident of getting a veto-proof majority on the Senate bill, including the DOE reorganization.
Although voicing concern about the nuclear agency, Sen. Carl Levin, D-Mich., said he too would vote for the changes because he didn't want to jeopardize the defense bill. The $288.8 billion defense measure includes military pay raises and a 4.4 percent overall increase in defense spending.
Sen. John Warner, R-Va., chairman of the Senate Armed Services Committee, and Sen. Pete Domenici, R-N.M., presented their case for the nuclear agency in a meeting with the president earlier this week.
"I left with the impression ... there is not uch fervor down at the White House for a veto," Warner said.
Domenici said he told the president "it's high time" to separate the nuclear weapons programs from the rest of the Energy Department. He said he and Warner made the argument that another alternative would have been to remove the nuclear program entirely from the Energy Department and put it under an independent agency.
Domenici rejected suggestions the reorganization would harm environmental or worker protection. The new agency would still be subject to all environmental laws, he said,.
But some critics of the proposal said the new agency would be insulated from the Energy Department's own officials responsible for ensuring that environmental and health protection requirements are met.