Centre for Disease Control official Wang Tsung-hsi confirmed that the couple, identified only their family name, Lee, had been transported from China's southeastern Xiamen city to Kinmen, a Taiwan-controlled island.
But Wang would not provide details.
CTI cable news network said the couple had been transported to Kinmen on a ship at a cost of 320,000 Taiwan dollars (9,756 US), and they might be flown back to the main island of Taiwan Tuesday.
The couple flew to the southeastern Chinese city of Nanjing from Kaohsiung in southern Taiwan on July 21 undetected by local health and immigration officials.
The husband is infected with multi-drug-resistant tuberculosis and his wife has an open tuberculosis, sparking a health scare as nearly 400 passengers were on the two Dragon Air flights with them from Taiwan to China via Hong Kong.
The CDC noticed the oversight three days later while matching the list of travellers recently departing the country with a TB patient database.
Taiwan's Department of Health warned it could take action against relatives of the Lees for trying to cover up their whereabouts while Mr. Lee would face a fine of between 10,000 and 150,000 Taiwan dollars (305 and 4,573 US) for violating regulations relating to patients with TB travelling on international flights.