"Today we learned from the media that Mr. Armstrong is choosing not to come in and be truthful and that he will not take the opportunity to work toward righting his wrongs in sport," Tygart said in a statement.
"At this time we are moving forward with our investigation without him and we will continue to work closely with WADA and other appropriate and responsible international authorities to fulfill our promise to clean athletes to protect their right to compete on a drug free playing field."
Failing to cooperate with USADA all-but dooms Armstrong's chance of reducing his life ban to an eight-year ban, only a possibility for providing substantial assistance to anti-doping authorities under WADA's code.
"We have provided Mr. Armstrong several opportunities to assist in our ongoing efforts to clean up the sport of cycling," Tygart said.
"Following his recent television interview, we again invited him to come in and provide honest information and he was informed in writing by WADA that this was the appropriate avenue for him if he wanted to be part of the solution.
"Over the last few weeks he has led us to believe that he wanted to come in and assist USADA, but was worried of potential criminal and civil liability if he did so."
Armstrong, 41, faces two major lawsuits that could be impacted by any testimony he gives under oath.
