The officials said Shin Shin gave birth Thursday afternoon and the mother and cub were said to be in good health, The Japan Daily Press reported.
The pandas are being monitored around the clock, officials said.
The Asahi Shimbun reported Shin Shin, who arrived at the zoo with mate Ri Ri in February 2011, is the first panda to give birth through natural breeding methods at the zoo. Three pandas were born at the facility in the 1980s through artificial insemination.
The gender of the newborn panda has not yet been released.