The move is aimed at preventing a pharmaceutical company from taking its own patent and then seeking money from researchers for their work, university officials said.
Teams at Kyoto University and at the University of Wisconsin at Madison in the United States last year discovered how to use skin to produce stem cells -- which can develop into various organs or nerves.
The finding was hailed by the Vatican and US President George W. Bush because it can circumvent an ethical row over conventional stem cell research using human embryos.
"It is important for the university to keep a patent so it can conduct medical research and treatment at low costs in the future," said Naoko Takasu, who is in charge of intellectual property issues for the university.
She said it was the first patent in the world for stem cells and that the university in western Japan would also seek patents in other major developed countries.
Shinya Yamanaka, the head of the research team, said he was "delighted" at the issuance of the patent.
"This is a first step," he said in a statement. "I will continue my utmost efforts in this research... so as to accelerate its practical application in clinical treatment."
Stem cell research is seen as having the potential to save lives by helping to find cures for diseases such as cancer and diabetes or to replace damaged cells, tissues and organs.
But religious conservatives argue that research on embryos destroys human life, albeit at its earliest stage of development.
Anticipating growing international competition in the field, Japan -- the largest spender on research after the United States -- in December announced a 10 billion-yen (92 million-dollar) plan to advance stem cell studies.
Another group of Japanese scientists said last month they had derived stem cells from wisdom teeth, opening another way to study deadly diseases without the ethical controversy of using embryos.