The boy is third in line to the throne, after Crown Prince Naruhito and Kiko's husband, Prince Akishino.
The Imperial Household Agency gave few details about the birth, which came by Caesarean section following pregnancy complications, and did not release the boy's name.
The agency said only that the baby was healthy and that he weighed about 2,558 grams (5.6 pounds).
Naruhito is the eldest son of Emperor Akihito.
Naruhito and his wife, Crown Princess Masako, earlier had a daughter, Princess Aiko, sparking the succession debate.
Many in Japan have thought that the birth of a boy to Kiko, who has two daughters, would take some of the pressure off Masako, who has struggled with depression -- and, at 42, is thought to have a slim chance of bearing more children.
Others, however, maintained that the succession law should be changed to allow Aiko to inherit the throne.
When the government previously proposed changing the law, polls showed that an estimated 70 percent of Japanese approved. Once Kiko's pregnancy was announced, however, public opinion switched, with Japanese saying it would be easier for Kiko to bear a son and resolve the succession issue for now.
The birth was cause for rejoicing in Japan, and media outlets broadcast continuing coverage about the event.
Kiko was hospitalized on August 16 after showing symptoms of partial placenta previa, in which part of the placenta drops too low in the uterus, The Associated Press reported.
The gender of the baby had been a closely guarded palace secret, though Japanese tabloids speculated the child would be a boy.
The last potential male heir born was Akishino himself, in 1965.
Reigning empresses have been rare in Japan, usually serving as stand-ins for a few years until a suitable male could be installed. The last reigning empress was Gosakuramachi, who assumed the throne in 1763, according to AP.
Debate over the succession law was divisive and emotional. Some conservatives proposed a revival of concubines to produce imperial heirs, and others argued that allowing a woman on the throne would destroy a precious Japanese tradition.
CNN's Atika Shubert contributed to this report
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