Pentagon reviews, he said, "found evidence of systematic problems that if not addressed could undermine the safety, security and effectiveness of elements of the force in the future."
Hagel told reporters that two reviews "show that a consistent lack of investment and support for our nuclear forces over far too many years has left us with too little margin to cope with mounting stresses."
The reviews came in the aftermath of a scandal in which airmen were caught cheating on a proficiency test for those who oversee intercontinental ballistic missiles.
Hagel said troops that worked with nuclear weapons often felt they had no career prospects.
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"The root cause has been a lack of sustained focus, attention, and resources, resulting in a pervasive sense that a career in the nuclear enterprise offers too few opportunities for growth and advancement," he said.
The Pentagon chief unveiled an "action plan" that includes reorganizing the command structure, restoring "pride" in the mission and more funding for equipment and additional personnel.
"We will need to make billions of dollars of additional investments in the nuclear enterprise over the next five years," he said.
Most of the recent scandals have been centered on the land-based missiles maintained by US Air Force crews, though the Navy also had a cheating scandal among sailors who work on submarines armed with nuclear missiles.
Hagel said the "good news" was that "there's nothing here that we can't fix" but he acknowledged that "we've taken our eye of the ball here."