The revelation comes in stark contrast to statements made by the U.S. Attorney for Southern California, Andre Birotte, who addressed his own criminal inquiry of Armstrong for the first time publicly on Tuesday. Birotte's office spent nearly two years investigating Armstrong for crimes reportedly including drug distribution, fraud and conspiracy -- only to suddenly drop the case on the Friday before the Super Bowl last year.
Sources at the time said that agents had recommended an indictment and could not understand why the case was suddenly dropped.
Today, a high level source told ABC News, "Birotte does not speak for the federal government as a whole."
According to the source, who agreed to speak on the condition that his name and position were not used because of the sensitivity of the matter, "Agents are actively investigating Armstrong for obstruction, witness tampering and intimidation."
An email to an attorney for Armstrong was not immediately returned.
Earlier Tuesday, during a Department of Justice news conference on another matter, Birotte was confronted with the Armstrong question unexpectedly. The following is a transcript of that exchange:
Q: Mr. Birotte, given the confession of Lance Armstrong to all the things --
Birotte: (Off mic.)
Q: -- to all thethings that you, in the end, decided you couldn't bring a case about, can you give us your thoughts on that case now and whether you might take another look at it?
Birotte: We made a decision on that case, I believe, a little over a year ago. Obviously we've been well-aware of the statements that have been made by Mr. Armstrong and other media reports. That has not changed my view at this time. Obviously, we'll consider, we'll continue to look at the situation, but that hasn't changed our view as I stand here today.
The source said that Birotte is not in the loop on the current criminal inquiry, which is being run out of another office.
Armstrong confessed to lying and using performance-enhancing drugs throughout his career in an interview with Oprah Winfrey.
Investigators are not concerned with the drug use, but Armstrong's behavior in trying to maintain his secret by allegedly threatening and interfering with potential witnesses.
Armstrong is currently serving a lifetime ban in sport handed down by the U.S. Anti-Doping Agency. He has been given a Feb. 6 deadline to tell all under oath to investigators or lose his last chance at a possible break on the lifetime ban.