The US television programme, 60 Minutes, has reported the breaches occurred during mock terrorist drills – one at the Y-12 nuclear complex in Oak Ridge, Tennessee and the other at Los Alamos National Laboratory near Albuquerque, New Mexico.
The scheduled tests showed long-standing security problems had not been adequately addressed despite the new terrorism risk.
"People should know that the Department of Energy facilities cannot withstand a full terrorist attack…a realistic attack, serious state-sponsored," nuclear security specialist and the person who conducted the mock drills, Richard Levernier said.
A spokesman for the National Nuclear Security Administration said the news release for the segment was "misleading at best and irresponsible at worst."
"Our nuclear materials are secure and it's irresponsible to suggest otherwise," spokesman Anson Franklin said.
"These tests are designed to find vulnerabilities before someone else does…it's wrong to suggest that terrorists could easily penetrate security at these sites."
Levernier said there was a 50% failure rate in the tests of factories and laboratories he conducted.
Reports of lax security included the disappearance of hundreds of electronic key cards and master keys at nuclear facilities.
Lawrence Livermore Laboratory near San Francisco failed to immediately report its missing keys, while at Sandia National Laboratories near Albuquerque, locks to missing keys had just been replaced after three years.