The commission said that it had no indications of the problems in the brachytherapy program when it arrived at the hospital and that its surveys are not detailed enough to have uncovered the flawed implants.

Soon after, the N.R.C. sent its own inspectors to Philadelphia. And the more the inspectors looked, the more they found. All told, 57 of the implants delivered too little radiation to the prostate, either because the seeds missed the prostate or were not distributed properly inside the prostate. Thirty-five other cases involved overdoses to other parts of the body. An unspecified number of patients were both underdosed in the prostate and overdosed elsewhere.

From December 2006 to November 2007, the nuclear commission found, 16 patients received seed implants in Philadelphia even though computer interface problems prevented medical personnel from determining whether those treatments had been successful. The V.A.’s radiation officials knew of the problem but took no action, the nuclear commission charges.

Investigators said they did not know how the unit made so many mistakes or why Dr. Kao decided to rewrite only two surgical plans. The doctors, according to the nuclear commission, believed “that since the patients were not having complications, the implant quality must be acceptable.”

The V.A. put too much trust in the contractors, said Darrell G. Wiedeman, a senior health physicist for the nuclear commission. “They claim they hired experts, the best that money could buy from the local university, so therefore they didn’t require a lot of training and oversight,” Mr. Wiedeman said at a recent meeting of the nuclear commission’s advisory board.

Susan Phillips, a senior executive at Penn’s medical school and health system, said Dr. Kao had voluntarily given up his clinical privileges there, though he continues to do research on campus. Dr. Kao did an unspecified number of brachytherapy procedures at the campus hospital with no apparent problems. A check of state and federal records over the last decade in Pennsylvania turned up no malpractice or disciplinary actions against Dr. Kao.

Back in West Virginia, Pastor Flippin said he continued to try to build up his small church while dealing with the side effects of his implant. After 21 years of serving his country, he had hoped for a better ending.

“It’s not fair,” he said. “Any veteran should expect more than what we’re getting.”