An 80-year-old woman was referred to our hospital due to a persistent productive cough. Acid-fast staining and a commercial Mycobacterium tuberculosis identification kit with TRC (TRC kit) were positive. However, a false-positive result on the TRC kit was suspected because Mycobacterium tuberculosis was not detected in the sputum culture. Finally, Mycobacterium shinjukuense was detected in an analysis of the rpoB and hsp65 gene sequences. As the diagnostic criteria proposed by the American Thoracic Society were met, a diagnosis of Mycobacterium shinjukuense lung disease was made. Following treatment with isoniazid, rifampicin and ethambutol with drug susceptibility, the patient's acid-fast culture became negative, and the areas of opacity improved.