French doctors say they tested Armstrong's hair, urine and blood in a March 17 test. They say they found no traces of drugs.
However, the agency, known as AFLD, said in a statement Thursday that a doctor charged with testing Armstrong last month claimed Armstrong "did not respect the obligation to remain under the direct and permanent observation" of the tester.
The AFLD says it is can impose sanctions on the American rider, but didn't indicate what they would be.
Armstrong announced a decision in September last year to come out of retirement and compete in the 2009 Tour de France - his effort to claim a record eighth Tour victory.
Armstrong's return from cancer to win the Tour seven consecutive times (already a record) made him a hero to cancer patients worldwide and elevated cycling to an unprecedented level in America.
The Tour "is the intention," Armstrong's spokesman Mark Higgins told The Associated Press last autumn, "but we've got some homework to do over there."