Eastern Health is apologizing for any distress the mistake caused, saying the error stemmed from a rare and isolated cross-contamination of a culture specimen.
It says medical treatment has been discontinued for the Grade 9 student as a result.
The health authority said last month that tuberculosis was detected in a student at Leary's Brook Junior High School in St. John's.
At the time, health and school officials said they were trying to identify students who may have been in contact with the youth.
Eastern Health says a review of laboratory information has since ruled out tuberculosis.
"While it is good news that this individual does not have TB, we apologize for any distress this occurrence may have caused to this individual and their family, as well as to those identified as close contacts," said Dr. Oscar Howell, vice-president responsible for the laboratory medicine program.
Tuberculosis is a disease caused by bacteria. Symptoms may include a cough that lasts for two or more weeks, chest pain, loss of appetite and fever.
Treatment normally involves taking medications for a period of six to 12 months.