The Tokyo-based Toshin Eisei Yobiko has introduced the system to six prep schools in the south.
According to the Yomiuri newspaper, students are enthusiastic about the system. But opponents say it is invasive and demeaning.
Education expert Professor Michio Nitta, of Tokyo University, was not surprised that jukus, as cram schools are known, were operating such a system.
"They are advanced in technology and management techniques. Authentication and ID technology is becoming a very important tool in the electronic market. I am not sure if the world of education can be excluded from this market."
Teachers who use the fingerprint scan to register classes said they preferred the new method over the traditional register. P> Toshin Eisei Yobiko also claim it is better at guarding student privacy, and more convenient than magnetic cards, which can be lost or stolen.
The business runs juku sessions at more than 800 sites around the country, using a satellite link-up to its headquarters in Tokyo, and plans to expand the system.
Japanese barristers have accused the Japanese government of neglecting children's rights. "It is no exaggeration to say that the human rights of the child do not enter through the school gates."
Japan has often been criticised for its poor record in upholding privacy. Until recently, all foreign residents were required to undergo traditional fingerprinting for identification purposes.
Only last month courts gave ex-pupils the right to have complete access to their confidential school records for the first time.