The top six infectious diseases which affected people were AIDS, tuberculosis, rabies, viral hepatitis, hand-foot-mouth disease and epidemic hemorrhagic fever, the ministry said in a statement.
About 41,929 AIDS cases were reported last year resulting in the death of 11,575 people while the number of deaths caused by tuberculosis (2,662), rabies (1,361), viral hepatitis (747) and epidemic hemorrhagic fever (104), all dropped from 2011.
Nearly seven million infectious disease cases were reported on the Chinese mainland, the statement said.
Both diseases are categorised as Class A infectious diseases under the Law on the Prevention and Treatment of Infectious Diseases.
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About 3.2 million Class B infectious disease cases were reported, with 16,720 fatalities.
Viral hepatitis, tuberculosis, syphilis, dysentery and gonorrhea were the most prevalent Class B infectious diseases, the statement said.
About 3.7 million Class C infectious disease cases were reported, with 594 fatalities, 567 of which were caused by hand-foot-mouth disease, it said.