Japan wants to decide by May where to relocate a US military air base at the centre of a row with its key ally Washington, the defence minister said Tuesday.

"We must work as quickly as possible," Toshimi Kitazawa told reporters as he outlined the new deadline for a decision.

Kitazawa admitted he supported a plan agreed with Washington in 2006 to move the US Marine Corps Futenma Air Station from an urban area to a coastal region within southern Okinawa prefecture.

The plan, however, is politically difficult to execute given opposition from residents and the Socialists in the ruling coalition, he said.

A new centre-left government took power in Japan in August after half a century of conservative rule, pledging to review past agreements on the US military presence and to deal with Washington on a more "equal" basis.

Prime Minister Yukio Hatoyama said on Tuesday he "understood" the US position, after Secretary of State Hillary Clinton urged Japan's ambassador in Washington to implement the 2006 agreement.

Hatoyama said last week that his decision would come in "several months" and that he was seeking an alternative site to the previously agreed area for relocation of the base.