An imperial household agency official told reporters that Kiko had given birth to the boy weighing 2.6 kilogram's after a caesarean operation. He said both the princess and the baby were doing well.
The boy will be third in line to the Chrysanthemum throne after his uncle and his father.
The birth is likely to dampen the debate on letting women inherit the throne - an idea opposed by conservatives eager to preserve a tradition they say stretches back more than 2,000 years.
No boys had been born into the family since Kiko's husband, Prince Akishino, in 1965, raising the possibility of a succession crisis. Crown Prince Naruhito and Crown Princess Masako have one child, 4-year-old Princess Aiko.
Junichiro Koizumi, the prime minister, had planned to revise the law to give women equal rights to ascend to the throne but Kiko's pregnancy had meant that the proposal was put on hold.
Koizumi's proposal, which was written by a panel of experts and prominent public figures, would have put Princess Aiko in line to the throne and let her first child follow her regardless of its sex.
Prince Naruhito is first in line to
the Chrysanthemum throne
Japanese emperors have no political authority but the monarchy remains popular in a country where symbolism and ritual are highly valued. The birth of a possible imperial heir had obsessed the media.
Eight empresses have ruled Japan, the last in the 18th century, but conservatives stress that they were stop-gap rulers.
In the first of a series of imperial rituals Emperor Akihito will give his fourth grandchild a ceremonial sword. He will be named next week.