But it will be the future of the five-decade-old Japan-US alliance that will be first on the US president's agenda as he lands in Tokyo.
Hatoyama has promised to halt a Japanese naval mission supporting the US-led war in Afghanistan, review basing agreements for 47,000 US troops stationed in Japan, and explore the possibility of a new Asian trading block that would exclude the US.
Al Jazeera's Rob Reynolds reports on the US president's first tour of Asia since taking office
Al Jazeera's correspondent Steve Chao, reporting from Tokyo, said that while much of the focus for Obama's visit has been on US-Japan security issues, the US president's main mission in Tokyo would be a wider-reaching one.
"He's trying to prevent what some are calling the 'Tokyo drift', which is a concern that Hatoyama and the newly elected government in Japan is moving towards a policy that is more independent of the US and away from the strategic alliance they have had for decades," he said.
Speaking to reporters on Friday morning ahead of the US president's arrival, Hatoyama said he was keen to ensure the meeting "shows the importance of Japan-US relations in a global context".
For his part, in an interview with Japanese TV, Obama acknowledged Hatoyama's election had been a "political earthquake" but he downplayed talk of any resultant friction in relations between Japan and the US.
Marine base deal
|Local residents in Okinawa have objected to the continued US military presence [Reuters]
"This is not a senior-versus-junior partnership," Obama said, speaking to Japan's NHK network before his departure from Washington.
"This is one of equals in which Japan has been an extraordinary contributor."
The major focus of tension centres on the future of the Futenma US Marine air base on Japan's southern island of Okinawa.
Under a 2006 deal the base is to be relocated to a less crowded part of the island.
Hatoyama however has said he wants the agreement to be reviewed and the base moved off the island, a suggestion the US has ruled that out saying it would undermine broader security arrangements that took more than a decade to negotiate.
Critics of the US presence in Japan have backed Hatoyama's suggestion, particularly residents of Okinawa which is home to more than half the US forces in Japan and a regular source of friction.
No breakthroughs are expected in the row during Obama's visit, although Hatoyama told reporters on Thursday he would tell the US president that he wants to resolve the issue soon.