White House spokesman Scott McClellan said Bush had signed into law the Energy and Water Development Appropriations Act of 2004 that contains funds for the Department of Energy and its nuclear programmes.
Overall, Congress allocated $6.3 billion for nuclear weapon activities in fiscal 2004 - $303 million more than last year, but $94 million below Bush's request.
The funds include $7.5 million to study the possibility of developing so-called "bunker-busting" nuclear bombs that officials say would enhance America's ability to destroy underground command and control centres and hidden arms depots.
An additional $6 million have been earmarked to study low-yield nuclear weapons that some experts believe could be useful in high-precision strikes.
Experts say a five-kilotonne or smaller nuclear explosive detonated, for example, right on a missile silo door will vaporize both the door and the missile inside.
The measures also includes $24.9 million to heighten readiness at the Nevada test site to enable it to conduct a nuclear test 24 months after the White House decides to do so.
The administration had been insisting on an 18-month readiness window, down from the current 36 months.
But Congress chose to tamp down the request in the face of vocal opposition from disarmament experts who have interpreted it as a sign of the administration's weakening determination to maintain a moratorium on nuclear tests.