Australian Foreign Minister Stephen Smith on Wednesday wished Japan's Prime Minister Yukio Hatoyama well following his resignation.

Smith acknowledged the role Hatoyama had played in strengthening the bilateral security and strategic partnership of the two nations.

"Prime Minister Yukio Hatoyama has been a good friend of Australia ... we wish him well for the future," Smith told the parliament.

The government looks forward to working with Japan's new leader, Smith said.

"The comprehensive economic, strategic and security partnership ... is one (which) ... continues."

Opposition foreign affairs spokeswoman Julie Bishop described Hatoyama as a man of "enormous integrity".

"It is always a difficult time when the national leader resigns, " Bishop told the parliament.

"Hatoyama is clearly a man of enormous integrity - he has accepted full responsibility for his inability to honor an election promise.

"His legacy will be one of enormous achievement in winning the election for his party ... and (of) dignity and integrity over this issue."

Hatoyama will step down after just eight months in office because of a broken election promise to move a U.S. Marine base off the southern island of Okinawa.

Hatoyama had been under growing pressure from within his own ranks to quit over the bungled handling of the relocation of the Marine Air Station Futenma.

Japan is Australia's second largest trading partner after China.