TOKYO - U.S. Defense Secretary Robert Gates pressed Japan on Wednesday to implement quickly a deal to reorganize the U.S. military presence in the country, an issue that could test ties with Tokyo's new government.

It is time to move on, Gates said at a news conference with Japanese Defense Minister Toshimi Kitazawa after they held talks on alliance issues. This may not be the perfect alternative for anyone, but it is the best alternative for everyone.

Gates left a possible compromise open by saying minor changes to the proposed position of two U.S. Marine runways on the coast of the southern island of Okinawa were a matter for Japan to decide.

A broad plan to reorganize U.S. forces in Japan was agreed in 2006 with Japan's long-dominant conservative party after a 1996 deal failed to gain support of local residents, many of whom associate the bases with crime, noise, pollution and accidents.

Kitazawa said he had pointed out the political difficulties involved in the deal, but added he felt spending a lot of time reaching a decision would not be healthy for the alliance.

Japan's month-old Democratic Party-led government has pledged to steer a diplomatic course less dependent on close security ally Washington.

That has prompted concern that security relations between the world's two biggest economies could suffer at a time when China's economic clout and military power are growing and North Korea remains as unpredictable as ever.

Under the circumstances in which uncertainties remain in this Northeast Asia region, I think it is imperative to maintain and develop our alliance even further, Prime Minister Yukio Hatoyama told Gates in a meeting earlier in the day.

OBAMA VISIT, NUCLEAR UMBRELLA

Gates' visit is intended to lay the groundwork for U.S. President Barack Obama's November 12-13 trip to Tokyo, his first as president to the key trade partner.

Gates stressed the benefits of the alliance for Japan, whose pacifist constitution restricts its military's role and which relies on the U.S. nuclear umbrella.

It seems to me that the primary purpose of our alliance from a military standpoint is to provide for the security of Japan. This defense umbrella has protected Japan for nearly 50 years, he said.

Japan is host to about 47,000 U.S. military personnel as part of the decades-old security alliance. Analysts say the troops' forward deployment is critical to the American military presence in the region.

The troop realignment pact is meant to reduce the U.S. military footprint on Okinawa while improving the ability of the two forces to cooperate.

Central to the deal is a plan to shift a U.S. Marine air base on Okinawa to a less crowded part of the island.

Hatoyama has said he wants the base moved off the island, but U.S. officials have ruled that out, saying it would undermine broader security arrangements that took years to negotiate.
Gates told reporters on his plane before arriving in Tokyo on Tuesday that he saw no alternative to the original plan, but Japan has suggested it needs more time to work out its stance.

Of course we absolutely don't plan on wasting time, Hatoyama told reporters after his meeting with Gates.

There isn't necessarily an agreement yet even within Okinawa, so while it's important to reach a final solution, I've said that we need more time.

Some analysts said the Pentagon's tough stance reflected the difficulty of adjusting to Japan's new political reality after half a century of almost unbroken rule by the Liberal Democratic Party (LDP), which put the alliance at the core of its diplomacy.

Hatoyama's Democrats trounced the LDP in an August 30 election.

The United States was the biggest destination for Japan's exports last year. The two countries accounted for about a third of global GDP in 2007, although analysts predict China could overtake Japan as the world's No.2 economy next year.

Few analysts expect the bilateral strains to spill over into economic ties between the two countries, but some say geopolitical uncertainty in the region could eventually affect investment decisions.

Gates later left for South Korea.

(Additional reporting by Yoko Kubota; Writing by Linda Sieg, Editing by Dean Yates and Paul Tait)