The announcement effectively breaks with past promises made by Hatoyama to relocate the facility outside the island.
Hatoyama had previously frozen a 2006 agreement with the US on moving Futenma to a less crowded part of the island, saying instead he wanted to move it off Okinawa entirely and straining ties with Washington.
The issue threatens the political future of Hatoyama, who has staked his job on settling the issue.
During Tuesday's visit, Hatoyama asked local residents to be open to a government plan that would keep some of Futenma's functions on the island, while possibly moving other functions further afield.
"We must ask the people of Okinawa to share the burden," he said.
However, he faces strong local opposition to keeping Futenma on the island and late last month, about 90,000 people joined a protest against the continued US presence.
|Strong local opposition remains to the US military presence on Okinawa [Reuters]
Local residents have long complained about the US bases, notably following a series of incidents allegedly involving US personnel, including the alleged rapes of a schoolgirl and a 19-year-old local woman.
Earlier this year, an anti-base candidate was elected as mayor of the northern town of Nago, the proposed site for the airfield's move.
During his visit Hatoyama was expected to present to Okinawa's governor and other local officials a government plan that roughly follows the 2006 deal to move Futenma to a location near Camp Schwab on the island's northeastern coast.
The government is also considering moving some of Futenma's functions to Tokunoshima island, north of Okinawa, but residents there held a massive protest this month and local officials rejected Tokyo's request for talks.
Japan, which committed to pacifism in its post-World War Two constitution, relies heavily on the US military presence for its security.