The President seeks to soothe relations with Tokyo strained by a row over a US military base.
Friday's visit is Obama's first stop on a nine-day, four-nation Asian tour, that will take him on to a regional economic summit in Singapore, then to China and finally to South Korea.
In Japan, Obama has met with Yukio Hatoyama, the country's new prime minister, who was swept to power in August vowing to build a more equal partnership with the US.
The two leaders held a news conference shortly after their meeting, and said they would continue to strengthen their alliance , Aljazeera.net reports.
Mr. Obama will hold talks with new Japanese Prime Minister Yukio Hatoyama aimed at improving ties with the longtime U.S. ally. Mr. Hatoyama led his center-left Democratic Party to power in August promising a much more independent relationship with the United States.
He campaigned on a pledge to move a U.S. Marine air base off the southern island of Okinawa, which would renege on an agreement reached in 2006.
The pact calls for relocating the Futenma base to a more remote part of Okinawa. Some residents have complained about noise, pollution and base-related crimes.
It was lso reported, the United States and Japan said they had agreed at a summit on Friday to expand cooperation in clean energy technologies in an effort to tackle climate change.
The two sides would work together in areas such smart grids, carbon capture and storage and nuclear energy, the two governments said in a joint statement after talks between U.S. President Barack Obama and Japanese Prime Minister Yukio Hatoyama in Tokyo.