The bill also contains $580 million for early work on a nuclear waste storage site at Yucca Mountain in the Nevada desert -- nearly the full amount Bush requested.
Negotiators shook hands on the bill as lawmakers stepped up efforts to finish their business for the year and adjourn by late November. To do that, they still must complete nine of the 13 spending bills for the federal budget year that started on Oct. 1.
They took a step in that direction recently when the House voted 417-5 to approve a $9.3 billion measure for military construction. The Senate is expected to approve that measure soon.
Bargainers on the energy-water bill provided $7.5 million for work on the bunker busters, bombs that would burrow through earth and rock to destroy underground targets. The administration wanted twice that amount.
The bill would provide all $6 million Bush proposed for research into ``mini-nukes'' of less than 5 kilotons. But $4 million of that amount would be provided only after the administration submits a report on the status of the country's nuclear weapons stockpile.
The lawmakers provided $11 million of the $23 million the Energy Department wanted for preliminary studies for manufacturing plutonium triggers for nuclear weapons. The department says the triggers are needed for the country's aging arsenal of warheads.
They also agreed to enough money to shorten the current three-year lead time needed to resume underground testing of nuclear weapons to two years, not the 18 months the administration requested.
The House version of the bill had made even deeper cuts in the nuclear weapons work, while the Senate had agreed to give all the administration had requested.
Rep. David Hobson, R-Ohio, and Sen. Pete Domenici, R-N.M., chief authors of the bill, called it a compromise. But opponents of nuclear testing complained that the final version went too far.
``I have the most profound objection to this reopening of the nuclear door,'' said Sen. Dianne Feinstein, D-Calif.
The measure also provided $580 million for this year's work at Yucca Mountain, an underground site envisioned as the ultimate home for 77,000 tons of used reactor fuel and other highly radioactive waste now accumulating around the country. Its cost is expected to exceed $50 billion.
Bush had requested $591 million for this year. Though Bush and Congress decided last year to proceed with the project, Nevada lawmakers are still trying to kill it.
One of the last disputes that had delayed the military construction bill was resolved when bargainers agreed to split earmarks -- money directed to specific home-district projects -- 53 percent for the Senate and 47 percent for the House. Earlier versions of the bill set aside roughly $700 million for Senate projects and $400 million for House earmarks.
Controlling the House, Senate and White House for a full year for the first time since 1954, the GOP had hoped to efficiently churn out all 13 annual spending bills by Oct. 1. That is when the government's 2004 budget year began.
But five weeks into the new fiscal year, fights over overtime pay for workers, media ownership, school vouchers and other issues have tripped up Republicans hoping to demonstrate their efficiency in running the government.
They are also trying to find about $3.6 billion in additional funds for updated voting equipment, AIDS assistance abroad, veterans health care and education.
The eight unfinished bills cover the budgets of 11 Cabinet level departments and dozens of other agencies.
To keep them functioning, the House voted 418-5 to temporarily finance those agencies through Nov. 21. Quick Senate passage was also expected for the third such bill lawmakers have passed this year.