Barack Obama greets new Japanese leader Naoto KanPage last updated at 0:41 GMT, Sunday, 6 June 2010 1:41 UK
Tokyo officials said Mr Kan had promised to make "strenuous efforts" to resolve the issue.
Japan's previous government resigned after failing to implement an election pledge to move the US base off Okinawa.
Many residents on the island resent the military presence.
Incidents including the rape of a 12-year-old Japanese girl in 1995 by three US servicemen have inflamed public opinion.
The White House said in a statement that the two leaders had agreed to work closely together on a number of issues.
"They emphasised the importance they each place on the US-Japan alliance," the statement said.
Washington did not mention the Futenma military base, which has been in place since World War II ended and has become crucial to US efforts to maintain a balance of power in East Asia.
The administration of former Prime Minister Yukio Hatoyama - who resigned last week - had tried to organise moving the base away from Okinawa.
But he failed to find an agreeable site and so proposed a compromise - to relocate it elsewhere on Okinawa.
Japan's Kyodo news agency reported that Defence Minister Toshimi Kitazawa had confirmed that Tokyo wanted to press ahead with the compromise plan.
The agency said Mr Kitazawa had told US Defense Secretary Robert Gates about the new government's intentions during talks on the sidelines of a security conference in Singapore.
Tokyo has not commented on the report.