A non-approved GM papaya variety has been found to have commingled with an Australian-made cheese that includes fruit pulp. The detected variety was from Thailand, while Japan has thus far approved only the Hawaiian GM variety "Rainbow." Since the beginning of this year, a total of eight cases of non-approved papaya have been detected, four of papaya in syrup imported from Thailand, one each of frozen papayas imported from China and Vietnam, and two cases of the Australian cream cheese containing fruit pulp. MHLW has publicized these as "examples of violations of the Food Sanitation Act due to imported foods."

Contravening the Cartagena Act, Kumamoto University and Nara Medical University have released GM microbes without taking the necessary treatment measures. On 26 February 2016, a researcher at Kumamoto University inadvertently discharged into the sewer system 50 ml of fluid containing GM lentivirus that was stored in a laboratory. The university says that waste water from the laboratory was diluted to over 100 times in the waste water tank, almost completely inactivating the lentivirus, and the water was further treated with chlorine and that therefore there was no leak of the lentivirus into the environment. In addition, at the same university, two cases were discovered of GM microbes being handled in laboratories with a low-level of biosafety, where they should normally be handled in a laboratory with a higher level of biosafety.

At Nara Medical University, waste water containing GM Escherichia coli bacteria deriving from overnight experiments had been flushed into the waste water system by laboratory assistants at a rate of about once every one or two months for over three years. The university has stated that since the water was treated with chlorine before flowing into rivers, the GM E. coli bacteria were inactivated.

In response to a consultation from MHLW in December 2015, the Food Safety Commission carried out deliberations in its specialist panel on prions concerning the abolition of BSE testing on cattle over 48 months of age that has been implemented up to now. The specialist panel concluded on 12 July that abolition of testing is reasonable and the Food Safety Commission has called for public comments. The reason given for the abolition is that "the difference between continuing and abolishing the current BSE testing for cattle over 48 months of age is minuscule and there are negligible risks of human health impacts." BSE was first reported in Japan in September 2001 and testing on all cattle was introduced the following month. A ban on beef imports from the USA was imposed when BSE was later found in that country. Pressure from the US government, however, caused imports to restart from August 2005 for meat derived only from cattle of 20 months of age or less. At the same time, domestic testing was considered to be unnecessary for cattle of 20 months of age or less, and this was further relaxed in July 2013 to cattle over 48 months of age.