WASHINGTON — An 82-year-old nun and two fellow pacifists who penetrated the defenses of one of the nation’s most important nuclear weapons facilities last week are due in federal court in Knoxville, Tenn., on Thursday to face charges of trespassing and spray-painting antiwar slogans on a building that houses nuclear bomb fuel. But the incident has also put the Department of Energy’s security system on trial.

The security breach, at Oak Ridge in Tennessee, has prompted the Department of Energy to reappraise security measures across its nuclear weapons program and private experts to criticize the agency’s safeguarding of nuclear stockpiles.

The activists, who got past fences and security sensors before dawn on July 28, apparently spent several hours in the Y-12 National Security Complex before they were stopped — by a lone guard, they told friends — as they used a Bible and candles in a Christian peace ritual. In a telephone interview, Sister Megan Gillespie Rice, of Las Vegas, said she was not sure exactly how long they were there. “It was dark; we couldn’t see our watches,” she said.

The problem for the National Nuclear Security Administration is how outsiders were able to get so close to more than 100 tons of highly enriched uranium, a material that could make thousands of atom bombs or be used by intruders to create a nuclear explosion on the spot. The security administration is a division of the Energy Department that was created to oversee the weapons program after security breaches were discovered in 1999. An administrator was fired in 2007 after additional security problems cropped up.