Most of the money, $2.7 billion, is to be spent on programs at the agency's weapons plants and laboratories in 12 states.
"This is not a result of current difficulties in our weapon plants," he said.
Energy Department inspectors have identified several problems at the nation's nuclear weapon plants since 1986.
It was the second time since October 1988 that the 37-year-old nuclear weapons plant had been shut down to improve safety and management.
This fiscal year, the department will spend $227 million in general plant funds, much of it at nuclear weapons plants.
There was no particular need to ask why the surviving Iraqi weapons plants were being exposed.
Such a reaction would be among the most severe that could occur at a nuclear weapons plant.
The weapons plants have been pouring nuclear poison into the atmosphere and land around them for years.
Last May, after studying her department's relations with the people who live around its weapons plants, she began a project to make amends.
China possibly suffered a serious accident at one of its biological weapons plants in the late 1980s.