"I bring greetings from President Obama," she said in a short statement after getting off the plane with her husband Edwin Schlossberg at Narita airport.
Japan hopes the 55-year-old daughter of late President John F. Kennedy will work closely with Mr. Obama to tackle some urgent U.S.-Japan matters, analysts said.
Her close ties to Mr. Obama come from playing a pivotal role during the Democratic presidential primaries in 2008 by endorsing him when Hillary Clinton was the lead candidate.
"What's important here is her strong pipeline with Obama and an ability to be able to pick up the phone and speak with Obama directly in the middle of the night for consultation on urgent matters," said Ryuichi Teshima, professor of diplomacy at Keio University in Tokyo.
As the first woman to serve as U.S. ambassador to Japan, Kennedy may also be a role model in a country that traditionally has restricted the role of women, said Toshihiro Nakayama, professor of international politics at Aoyama Gakuin University.
"I am also proud to carry forward my father's legacy of public service," Kennedy said. "He had hoped to be the first U.S. president to visit Japan. So it is a special honor for me to be able to work to strengthen the close ties between our two great countries."
Kennedy's arrival comes a week before the 50th anniversary of her father's death at the hands of Lee Harvey Oswald. CBSNews.com will stream the full broadcast coverage from 1963 of JFK's assassination, beginning at 1:40 p.m. Eastern time on Friday, Nov. 22, 2013.
U.S.-Japan relations are generally on an even keel, but Obama and Japanese Prime Minister Shinzo Abe are not as close as some would like. "The chemistry is off, possibly because Obama does not support the right-wing views Abe holds," Teshima said.
Major bilateral issues include the Trans-Pacific Partnership trade talks, the relocation of a U.S. military base on Okinawa and a revamp of defense cooperation guidelines between the two countries.
U.S. ambassadors to Japan can be grouped into three categories, Nakayama said. They are big political names, Japan experts and those with close ties to the president. Former U.S. Vice President Walter Mondale and former Senator Mike Mansfield fall into the first type. Edwin Reischauer, President Kennedy's envoy, would be the second.
Nakayama puts Caroline Kennedy, an attorney and author, in the third group, along with her predecessor, John Roos, a Silicon Valley lawyer and Obama fundraiser, and Tom Schieffer, who was George W. Bush's business partner in the Texas Rangers baseball team.