The news on Tuesday came just as parliament was planning to debate whether women should be allowed to inherit the throne.
Kyodo news agency said the 39-year-old princess would probably give birth in September or October.
No boys have been born into the imperial family since 1965, when Kiko's husband, Prince Akishino, the second son of Emperor Akihito, 72, was born.
The current law allows only males descended from emperors to become sovereign.
Crown Prince Naruhito and his wife, Masako, have one child, the four-year-old Princess Aiko.
Masako, 42, has been unable to perform most of her official duties for more than two years due to a mental disorder caused by the stress of adapting to rigid royal life, including, royal watchers say, pressure to bear a son.
Under the current law, if the newborn is a boy, he would be third in line to inherit the Chrysanthemum throne after his father and Crown Prince Naruhito.
Both of Kiko's two children are daughters.
If confirmed, the pregnancy is likely to boost conservative opposition to revising Japan's imperial succession law to let women inherit the throne, a legislation Junichiro Koizumi, the prime minister, has said he wants to enact in the current session of
"I will still submit the law [for the revision] ... during the current session of parliament"
Japanese prime minister
parliament ending in June.
"I will still submit the law [for the revision] ... during the current session of parliament," Koizumi told a parliamentary panel after the news broke. He said that it would be difficult to preserve a stable succession if only males could reign.
Those opposed to changing the succession law want to maintain a male line they say stretches back more than 2000 years.
If the succession bill is passed, Aiko would eventually become Japan's first reigning empress since the 18th century.