The ministry believes the dust and toxic substances that make up the smoke could cause cancer.
Phonthep Sirinarangsan, chief of the Department of Health, said carcinogenic substances are emitted from the burning of glue, sawdust and perfume present in joss sticks.
Incense smoke also contains pollutants such as sulphur dioxide, nitrogen dioxide, carbon monoxide and carbon dioxide, which can cause sore eyes, drowsiness and headaches.
Some people may even fall unconscious if exposed to the smoke for long periods, Dr Phonthep warned.
Consumers are advised to use short joss sticks, place their incense pots in well-ventilated areas and wash their hands after using incense. If necessary, they should rinse out their eyes as well.