Researchers at the government-backed National Institute of Advanced Industrial Science and Technology said they created stem cells of the type found in human embryos using the removed wisdom teeth of a 10-year-old girl.
"This is significant in two ways," team leader Hajime Ogushi told AFP. "One is that we can avoid the ethical issues of stem cells because wisdom teeth are destined to be thrown away anyway.
"Also, we used teeth that had been extracted three years ago and had been preserved in a freezer. That means that it's easy for us to stock this source of stem cells."
The announcement follows the groundbreaking discovery by US and Japanese scientists last year that they could produce stem cells from skin, a finding that was hailed by the Vatican and US President George W. Bush.
Research involving embryonic stem cells -- which can develop into various organs or nerves -- is seen as having the potential to save lives by helping find cures for diseases such as cancer and diabetes.
But studies on embryos are strongly opposed by religious conservatives, who argue that such research destroys human life, albeit at its earliest stage of development.
In the new research, cells were extracted from the wisdom teeth and developed for about 35 days.
The researchers then tested them and found that they were stem cells, which can develop into various other kinds of human cells, Ogushi said.
As with last year's skin cell discovery, the Japanese researchers said it would take time to put the use of wisdom teeth into practical use.
Ogushi estimated it would take at least five years to put the method into clinical use such as trial treatments of congenital bone disease.
"Because extractions of wisdom teeth are commonly operated in dental clinics, we can expect a lot of donors of stem cells," he said.
"That enable us to create stem cells of various genetic codes, eliminating the risk that a body of a patient would reject transplanted tissues or organs," he added.
He was hopeful that the method would produce stem cells of various genetic codes -- reducing the risk that patients' bodies would reject transplanted tissues or organs.
Theoretically, people who give up their wisdom teeth in their youth could use the stem cells later in life if they need treatment.
The research takes points from last year's skin cell breakthrough, which was a collaborative effort by researchers at Kyoto University and the University of Wisconsin at Madison.
The Kyoto University team, led by Shinya Yamanaka, generated human stem cells by introducing four genes into a sample of human skin.
Ogushi introduced three of of the four genes identified by Yamanaka into the wisdom teeth.
Japan, the largest spender on scientific research after the United States, in December announced a 10 billion-yen (92 million-dollar) plan to advance stem cell research over five years.