The United States Anti-Doping Agency (USADA) had lobbied the Justice Department to join the lawsuit.
USADA officials had been in separate negotiations with Armstrong to get him to reveal more details of doping in the sport in exchange for a possible reduction in the length of time he is banned from competition. The agency has already banned him from the sport for life and stripped him of his Tour de France titles.
But on Wednesday, Armstrong refused for a second time to testify under oath before the USADA.
After denying doping accusations for years, Armstrong in January admitted to using performance enhancing drugs in a televised two-part interview with Oprah Winfrey.
In that interview, Armstrong said he and his teammates could not have won the Tour without relying on a mix of EPO, transfusions, human growth hormone and testosterone.
He told Winfrey that at the time he didn’t see it as cheating because doping was so widespread in cycling.
“I viewed it as a level playing field,” he said.