The Senate yesterday overhauled the program that just five years ago was billed as the solution to the nation's growing accumulation of high-level nuclear waste.

The revamped search for an underground radioactive waste site is the most contentious feature in a $15.9 billion appropriations bill providing money for energy and water development programs in the fiscal year that began Oct. 1.

Approved by 86 to 9, the legislation would scrap the delicate, hard-won compromise reached by Congress in 1982 to create two waste repositories, one in the West and the other in the East or upper Midwest. The new Senate plan, advocated by Sen. J. Bennett Johnston (D-La.) and the Reagan administration, would all but scrap the eastern site and tilt the selection process toward placing the western repository at Yucca Mountain, Nev.

The plan also would authorize an above-ground facility to serve as an interim cooling and packaging area for waste headed for the permanent facility. The Energy Department has proposed Oak Ridge, Tenn., for the so-called monitored retrievable storage facility.

In an effort to sweeten the pot for states getting nuclear waste, the bill would provide $100 million a year for hosting a permanent repository and $50 million a year for temporarily storing the waste.

The Senate proposal faces an uncertain future. The House version of the spending bill proposes no changes in the 1982 program and members of the House influential on nuclear issues have criticized the Senate plan. Johnston says there are some 40,000 metric tons of nuclear waste, much from power plants, awaiting disposal. The waste, growing by about 3,000 metric tons a year, is considered dangerous for 10,000 years.

Working under the 1982 plan, the Energy Department has tabbed Yucca Mountain; Hanford, Wash., and Deaf Smith County, Tex., as final candidates for the first repository, which was supposed to open in 1999.

Detailed studies as to their geological suitability are supposed to be conducted simultaneously. But Johnston says that $3.9 billion can be saved if studies focus on one site at a time and if the first site is deemed suitable, the need for further studies is eliminated.

Other sections would provide $4.26 billion to the Army Corps of Engineers and the Bureau of Reclamation to build, operate and maintain water projects in fiscal 1988.

The Senate proposes to begin construction on 22 new corps projects, nine more than requested by the administration and 21 fewer than proposed by the House in its bill, which President Reagan has threatened to veto.