This is Mr Gates' first trip to Japan since Mr Hatoyama came to power
US Defence Secretary Robert Gates has urged Japan to honour a 2006 agreement on relocating a US airbase to another part of the island of Okinawa.
After talks with Japan's new Prime Minister Yukio Hatoyama, Mr Gates said the deal should be acted on quickly.
Japan has said it wants to review the deal, and recently suggested the base could be moved off Okinawa altogether.
Both countries are reviewing relations, critical to regional security, under their new administrations.
On the campaign trail, Mr Hatoyama said he wanted a more equal security relationship with the US than Japan had previously - and promised a more "autonomous" foreign strategy.
But during Wednesday's meeting, Mr Hatoyama tried to reassure Mr Gates that US-Japan security relations were still very important to the Japanese.
"Under the circumstances in which uncertainties remain in this North East Asia region, I think it is imperative to maintain and develop our alliance even further," he said.
The US has been Japan's key security ally since the end of World War II, and there are currently some 47,000 American troops in the country, most of them on the island of Okinawa.
A broad plan to reorganise US forces in Japan was agreed in 2006 with the previous Japanese administration, but has yet to be implemented.
The agreement would see Japan fund a replacement base in Okinawa and the transfer of 8,000 US marines to Guam by 2014.
Mr Gates is eager for the agreement to be acted upon as soon as possible.
"Our view is this may not be the perfect alternative for anyone but it is the best alternative for everyone," he said at a joint press briefing with Mr Kitazawa.
"This is the time to move on," he added.
But Mr Hatoyama had promised as part of his election campaign to re-examine the conditions of the deal - which many people on Okinawa object to, as they want the US presence there to end.
"Our new government has its own thoughts. We would like to spend time and reach a good result," Kyodo news agency quoted Mr Hatoyama as saying ahead of his meeting with Mr Gates.
The US is keen to get an agreement before President Barack Obama visits Tokyo next month.
Another sticking point between the US and Japan is the new government's decision to end an Indian Ocean refuelling mission in support of the war effort in Afghanistan. Japan wants to offer more civilian aid instead.