The NRC said it was particularly concerned that even after the Philadelphia hospital's problems were discovered, the VA missed similar issues at other hospitals.
Still, the nuclear agency declined to take the most severe action against the VA: removing the VA oversight of radiation safety at all its hospitals.
The VA did not respond to requests for comment.
Rep. John Adler (D, N.J.), the area's only congressman on the House Committee on Veterans' Affairs, said: "The NRC has found widespread medical misconduct throughout the VA's brachytherapy program. It is time the VA acknowledges and fixes their mistakes."
The NRC said it would hold a public meeting "to further discuss the actions" needed to improve the VA's radiation safety oversight.
The fine imposed Monday stemmed from two violations; the brachytherapy programs lacked procedures to ensure the implants followed a preoperative plan, and they failed to notify the NRC within 24 hours of a failed procedure.
"These violations should have been identified by the [VA] during their own independent inspections," said Mark Satorius, the NRC regional administrator for Region III, which oversees the VA's radiation safety program.
"We expect the [department] to ensure all facilities with prostate brachytherapy programs not only fully understand and follow NRC regulations but also rigorously implement their oversight role to ensure medical procedures with nuclear materials are delivered safely."
Prostate brachytherapy involves implanting dozens of tiny radioactive seeds into the acorn-sized gland to kill cancer cells over several months. It is effective care if done correctly.
In Philadelphia, 97 of 114 veterans treated with brachytherapy got improper doses of radiation between February 2002 and June 2008, when the program was shut down.
Records show that the VA's program here was flawed from its earliest patients and that doctors and officials repeatedly missed chances to fix it.
Now the VA has 30 days to accept or challenge the $39,000 fine. After that, the NRC will set a date for the public meeting to further examine oversight.
Contact staff writer Josh Goldstein at 215-854-4733 or email@example.com.