After months of political controversy over suspected Chinese espionage, the Senate overwhelmingly passed legislation yesterday creating an agency to manage the nation's nuclear weapons plants in the most far-reaching reorganization of the Department of Energy since its creation 22 years ago.

Sen. Pete V. Domenici (R-N.M.), the plan's primary architect, said creating the National Nuclear Security Administration would streamline management, improve security and elevate the nuclear weapons complex within the Energy Department's chaotic bureaucracy, which oversees everything from warheads to windmills.

"The rules and regimes that govern the rest of the Department of Energy," Domenici said, "cannot be simply and blindly applied to our vital national security programs."

The reorganization proposal now goes to President Clinton as part of a $289 billion defense authorization bill that contains a popular 4.8 percent pay raise for military personnel, which makes a veto unlikely.

Creating the nuclear security agency, whose administrator would have to be confirmed by the Senate, represents Congress's most dramatic response to China's alleged theft of such nuclear secrets as the design of the W-88, the smallest and most advanced warhead in the U.S. arsenal.

The government has not brought any charges against its prime suspect, Wen Ho Lee, a Chinese American scientist who was fired in March from his job in the top-secret X Division at Los Alamos National Laboratory. Yesterday, U.S. officials said the FBI is widening its investigation to include other potential suspects at various facilities.

The new agency will supervise the nationwide network of laboratories and plants that research, design, assemble and maintain America's nuclear weapons. Together, the nuclear complex employs more than 30,000 people and has a budget of about $6 billion a year.

Although the agency will be part of the Energy Department, it will have a high degree of autonomy, like that of the Federal Aviation Administration inside the Department of Transportation and the Internal Revenue Service inside the Treasury Department.

Energy Secretary Bill Richardson and other Democratic critics of the plan have argued that it will give nuclear weapons laboratories more autonomy when what they really need is tighter oversight.

"While Congress had the right idea, it passed the wrong reorganization plan," Brooke Anderson, Richardson's spokeswoman, said after the vote.

The Clinton administration also has expressed concern that the reorganization could dilute Richardson's authority, but the White House has not threatened a veto. "I think we continue to have concerns" about the reorganization, White House spokesman Joe Lockhart told reporters. "There's obviously things in the bill that we like. So we're going to look at this, and when we have a decision, we'll let you know."

Daniel S. Greenberg, a visiting scholar at Johns Hopkins University who has written extensively about the Energy Department, said he is skeptical about the prospects for genuine reform in what he considers the government's most dysfunctional department.

"The problems of DOE are deep in its genes," Greenberg said. "The new agency is still going to be inside DOE and ultimately answerable to the secretary. . . . We're going to have more guards at the door. But I don't see intrinsically how much has changed."

The department has been responsible for nuclear weapons since it was created in 1977 as the successor to the Atomic Energy Commission, which had been formed immediately after World War II so the nation's nuclear arsenal would be in civilian, not military, hands.

Greenberg said a more meaningful Energy Department reorganization would have ended this "fiction" of civilian control and turned all of the department's weapons responsibilities over to the Pentagon, which is better equipped to safeguard secrets.

Greenberg also said the department has long been been plagued by internal "schizophrenia" that comes from safeguarding the nation's darkest nuclear secrets while trying to foster open scientific exchange at the national laboratories.

Nuclear Weapons Complex

Here are major facilities that produce and maintain the U.S. nuclear arsenal.

* Lawrence Livermore National Laboratory

Stockpile stewardship and maintenance, arms control, waste management.

* Nevada Test Site

Stockpile stewardship and maintenance, nuclear testing, disposal.

* Sandia National Laboratories

Weapons design, arms control, waste management.

* Los Alamos National Laboratory

Stockpile stewardship and maintenance, arms control, waste management.

* Pantex Plant

Weapons assembly, dismantling, disposal.

* Kansas City Plant

Weapons construction.

* Y-12 Plant, Oak Ridge National Laboratory

Nuclear materials production, arms control, disposal.

* Savannah River Site

Nuclear materials production.