The train was travelling from the Austrian border up to Berlin early on Tuesday morning and was only carrying refugees, the Süddeutsche Zeitung reports.
Police stopped its journey at Pasing, a station on the outskirts of Munich, at around 1am after medical teams on board were alerted to a passenger who had been coughing heavily for the first stretch of the journey.
Suspecting that he was suffering from a lung infection, the medics alerted the authorities.
After he was taken to hospital it was confirmed that the man was suffering from a severe case of tuberculosis.
Tuberculosis is an infectious disease which can be spread through the air through coughing or sneezing. If left untreated it can be fatal.
In Germany it is relatively rare, with only a few thousand cases reported each year. In parts of Asia and Africa it is much more prevalent.
According to information from the World Health Organization (WHO) there are around 9 million cases of the disease globally each year, 1.4 million of which prove fatal.
It is unclear at this point where the man came from or what his route into Germany was. Authorities in Bavaria are now trying to reconstruct his journey and establish whom he had contact with.
It is compulsory in Germany for all refugee reception centres to conduct a tuberculosis screening for new arrivals.