The United States and Japan said Thursday Tokyo would pay a third of the cost of Washington pulling thousands of Marines out of Japan as it reduces its heavy military presence on Okinawa.

US Secretary of State John Kerry, Secretary of Defense Chuck Hagel, Japan's Foreign Minister Fumio Kishida and Defense Minister Itsunori Onodera signed the protocol amending the 2009 Guam International Agreement, as part of a meeting on the two countries' alliance.

Changes include "clarifying that Japan will contribute up to $3.1 billion in Fiscal Year 2012 US dollars in direct cash contributions to develop facilities and infrastructure in Guam and the Commonwealth of the Northern Mariana Islands", the state department said.

It accounts for 36 percent of the projected $8.6 billion cost of the relocation.

The protocol also affirmed the US government "shall favourably consider requests by the government of Japan to use training areas in Guam and the Commonwealth of the Northern Mariana Islands."

In a 2012 agreement, the United States said it would pull 9,000 Marines out of Okinawa -- 4,000 of whom would go to Guam and 5,000 to Hawaii and on rotations to Australia -- as it seeks to ease a long-running standoff over the future of its huge military presence in one of its top Asian allies.

Okinawa continues to be a source of tensions in a security relationship that both sides see as indispensible.

Around half of the 47,000 US service personnel in Japan are based on the strategically located island chain, which is nearer to Taiwan than it is to Tokyo.

The United States had agreed in 2006 to shift its Futenma air base -- a longtime source of grievance as it lies in a crowded urban area -- to a quiet stretch of seashore, with Marines leaving Okinawa.

The Futenma relocation has been stuck due to local opposition, but the two governments have agreed to treat the Marine relocation separately.

The planned Marine move, which is due to begin in the early 2020s, is part of a wider rebalancing of US military assets in the region under President Barack Obama's trumpeted "pivot" to Asia.