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The discovery of a plutonium leak in one of the nation's oldest and largest nuclear waste dumps has presented both a problem and an opportunity in the federal government's effort to deal with a legacy of dangerous wastes from the buildup of the nation's nuclear arsenal.

Against a pristine panorama of mountains, desert and brilliant sky in southeastern Idaho, engineers using delicate monitoring equipment have confirmed that traces of plutonium have drained from shallow waste pits at the Radioactive Waste Management Complex. They are moving through rock layers toward a vast underground water reservoir that supplies thousands of southern Idaho residents. The deadly elements have been confirmed 110 feet beneath the waste site and tests indicate they are as deep as 240 feet, nearly halfway to the reservoir.The leaks at the 36-year-old waste site, part of the government's Idaho National Engineering Laboratory, were first identified in June 1987. It is a problem that has arisen in 12 other states at the national laboratories and industrial plants that spent almost five decades making nuclear weapons for the military, leaving behind radioactive waste that could take until the 22nd century to clean up.

At the same time, the Idaho plant is one of those at which the government is attemping to develop methods for stopping leaks at nuclear waste sites as well as developing methods for disposing of other radioactive substances, including contaminated soil.

"We're going to be in this cleanup business 50, 100, 150 years from now," said George Kritz, a physicist and director of the Energy Department's hazardous waste and remedial action division in Germantown, Md.

The Energy Department said last month that it would cost a total of about $100 billion to determine how much waste there is at sites nationwide, to contain it and to clean it up. This is an effort that emerged this year as one of the department's principal missions.

In the fiscal year 1988, the department will spend $895 million to manage its radioactive wastes, or nearly 12 percent of the $7.5 billion budget for nuclear weapons production. Two years earlier the amount was $618 million, 8 percent of the department's weapons budget.

Engineers in Idaho say the particles of plutonium that have penetrated to the deep rocks do not pose an immediate threat to any of the 10,000 employees at the Idaho laboratory, the 40,000 residents of Idaho Falls, or to any other citizen. Health specialists agreed.

But federal engineers said they are concerned about future generations. Plutonium remains radioactive for 250,000 years and even microscopic particles can be lethal if they are inhaled or swallowed. If enough of the man-made element penetrates to the underground reservoir, the aquifer's use to farmers or households could be limited or ruined, the federal authorities acknowledged.

"We don't expect that to happen," said James E. Solecki, director of waste management at the Idaho laboratory. "The levels of plutonium we've found are very low, about the same as what you'd find on the ground in New York or Washington from atmospheric testing in the 1950s. We're watching the situation very carefully."

According to studies by the General Accounting Office, the investigative arm of Congress, the Idaho site is one of 1,300 in which wastes from atomic weapons production were buried or stored. The agency said many had become substantial environmental and public health threats. Here are some of those situations:

Radioactive substances from waste pits holding 11 million gallons of uranium at an Energy Department plant in Fernald, Ohio, are leaking into an aquifer and have contaminated wells a half-mile south of the facility.

More than 500,000 gallons of highly radioactive liquids have leaked from tanks at the Hanford Reservation near Richland, Wash. Other radioactive substances have contaminated water under the ground. In another part of the reservation, billions of gallons of contaminated water were poured into the ground and a steady stream of radioactive tritium is flowing into the Columbia River.

Chemicals and radioactive material have contaminated the aquifer beneath the Savannah River Plant near Aiken, S.C., and are now present at levels 400 times greater than what the Government considers safe. The General Accounting Office and environmental and scientific groups say the 300-square-mile region could be irreversibly contaminated.

"The nation faces a formidable task to clean up thousands of sites owned by the federal government at which uncontained hazardous and radioactive wastes are contaminating soil and ground water," Dexter Peach, assistant comptroller general of the GAO, told a House Energy and Commerce subcommittee last month. "Cleaning up the Energy Department's nuclear facilities may be the government's biggest challenge."

The department is completing a $1.3 billion plant to turn highly radioactive liquid wastes stored at the Savannah River Plant into glass logs for safer storage and a similar plant is planned for the Hanford Reservation. A $700 million waste repository is under construction in New Mexico to permanently store plutonium-contaminated wastes.

The agency is also studying how to decontaminate old reactors and production facilities that have been abandoned. Since 1982, workers clad in protective suits and outfitted with acetylene torches have been dismantling a laboratory building in Miamisburg, Ohio. Taking the plutonium-contaminated laboratory apart by hand and transporting the pieces to Idaho or New Mexico will not be completed until the mid-1990's when the cost is expected to total $50 million.

In interviews, government experts said the atomic waste disposal program will tax the agency's technical abilities. One of the sites where the agency hopes to learn how to plug nuclear leaks is at the 144-acre Radioactive Waste Management Complex in Idaho.

Set down in the shadows of the jagged Lost River Range and marked by a pair of white inflatable buildings, the desert complex resembles an encampment in a lonely lunar valley. Federal officials said that only the Soviet Union could have a plutonium waste site that is larger than the one cleared from sagebrush and juniper in the southwestern portion of the 890-square-mile atomic reservation.