It is also believed he may have made another drug known as 5F-QUPIC last year.
The professor allegedly claimed he set the task to help his students’ “learning”.
It is suspected 11 former students were involved in producing the drug, the news agency reported.
The case, which also involves an assistant professor, is said to have been passed from the regional drug enforcement authority to prosecutors.
Tatsuya Mizogami, president of the university, “sincerely apologised” to students and parents.
In Japanese law, a researcher must obtain a licence from regional government authorities to make narcotics for academic research.
The professor is understood to have been carrying out research into drugs that cause hallucinations or have a stimulant effect.
MDMA is a synthetic psychoactive drug, commonly used in party drug ecstasy, which is taken to give a heightened sensation of energy, empathy and pleasure.
5F-QUPIC, also known as 5F-PB-22, is a designer cannabis-like drug.
The case of the Matsuyama University professor has echoes of the character Walter White in US TV series Breaking Bad.
White, played by actor Bryan Cranston, is a chemistry teacher who begins making and selling methamphetamine to secure his family’s financial future after learning he has inoperable lung cancer.