The Senate approved 63 to 30 yesterday a major overhaul of the nation's high-level nuclear waste program, virtually choosing Nevada as the likely site for a permanent repository while scuttling plans to build an identical facility in the upper Midwest or the East.

The new plan, drafted by Sens. J. Bennett Johnston (D-La.) and James A. McClure (R-Idaho), includes a $100 million annual federal payment to the repository state and $50 million per year to the state in which an interim cooling and packaging facility is built.

Though the legislation, an amendment to a $16 billion energy and water development bill, does not specify Nevada's Yucca Mountain as the first choice for a permanent burial site for spent nuclear fuels and other high-level wastes, it clearly points in that direction.

Johnston's measure calls for exploration to be done in sequential, rather than simultaneous, order, in hopes that the first site to undergo major testing will prove suitable for the repository -- and that work at the other two sites can be canceled at a savings of $3.9 billion.

Technically, it would be left to the Energy Department to decide by Jan. 1, 1989, which site should be explored first. Under current law, Yucca Mountain, as well as sites at the Hanford nuclear reservation in Washington state and Deaf Smith County, Tex., are candidates for exploratory work -- including the drilling of deep shafts -- costing nearly $6 billion.