The divisions are so sharp that Crown Princess Masako, pleading a cold, did not once visit the ailing Emperor Akihito, who turns 78 this month, as he lay for 19 days in the University of Tokyo hospital with bronchitis.
The estrangement between the emperor and the couple comes in the twilight of Akihito's reign and foreshadows profound changes in the ancient dynasty.
Long rumoured, but seldom confirmed, the troubles of the monarchy last week moved from the gossip pages of weekly magazines into the staid columns of Japan's most respected newspapers.
|Prince Akishino and his wife, Princess Kiko|
Supporters of the crown prince and princess, who both studied at Oxford, had hopes they would refresh the court with a modern, cosmopolitan touch - hopes that foundered on stony traditions.
Instead, Japan has endured the private anguish of its crown princess, who has been receiving psychological care for eight years and seldom appears at royal engagements. Masako was ostracised by courtiers when she tried to break with protocol, failed to produce a male heir to the throne and then went into seclusion after a nervous collapse.
The royal couple have a daughter, Aiko, 10, who cannot accede to the chrysanthemum throne under a rule barring women. Crown Prince Naruhito has defended his wife against criticism and this has led to an erosion of his stature in the eyes of the emperor and the rest of the family.
Instead, Prince Akishino, his younger brother, has advanced in favour as the father of the male heir to the throne, Prince Hisahito, now aged five. Hisahito's birth 12 years after his parents' last child ended parliamentary discussion of reforms to allow Aiko to succeed.
Now taboos are crumbling after the younger prince spoke publicly about the distance between the brothers.
"Unfortunately, we do not have the opportunity to interact on many occasions with the crown prince and princess," Akishino told a press conference to mark his 46th birthday.
He remarked the imperial grandchildren rarely saw each other, even though they all lived on the leafy Akasaka estate in central Tokyo. "There have only been a limited number of opportunities for our children to be together," Akishino said.
According to the Asahi Shimbun, a leading daily paper, his comments "give the impression that the crown prince and his family have become isolated within the entire imperial family".
It said the elderly emperor saw far more of little Hisahito, who is a passionate collector of insects, and joined him on expeditions in the imperial palace gardens.
"That may reflect a special bond towards Hisahito, who is the first and only grandson," the paper commented, adding: "The emperor and empress ... want to pass on the future to (Akishino's) children ... that is because they feel they can no longer depend on Masako, who rarely makes public appearances due to an 'adjustment disorder'."