"He was told in no uncertain terms not to take a flight back," said Cetron.
Despite the warning, he returned to North America on May 24 aboard Czech Air Flight 0104 from Prague to Montreal and then drove into the US.
Earlier, on May 12, he had travelled to Europe on a flight from Atlanta to Paris, aboard Air France Flight 385.
The CDC urged people on the same flights to get checked for tuberculosis.
Cetron reached the man once he was back in the US, at which point he voluntarily went to a New York hospital, then was flown by the CDC to a hospital in the Atlanta area.
He has been placed in respiratory isolation but is not facing prosecution, health officials said, adding that they were working with the airlines to contact passengers who were sitting next to him or in the rows around him.
Passengers who should be tested will be contacted by health officials from their home countries, Cetron said.
But passengers are not considered to be at high risk of infection, Cetron said, as tests indicated that the man had only a low amount of the TB bacteria in his system.
The man, who was infected with "extensively drug-resistant" TB, also called XDR-TB, told health officials he was not coughing during the flights.
Last year there were two US cases of the strain.
Meanwhile, globally in 2006, there were an estimated 1.6 million deaths from TB, according to the World Health Organisation.
It is the first time since 1963 that the US government has issued a quarantine order.
According to the CDC, the last such order was to quarantine a patient with smallpox.