Protests against American military presence in Japan continued on Saturday, as the country’s defense minister lodged a formal complaint over the latest case of alleged murder and rape of a young Japanese woman by a US military base employee.

Gen Nakatani visited the US Kadena Air Base on Saturday to formally protest the alleged crime to its commander Lt. Gen. Lawrence Nicholson.

"I deliver a strong message of regret and at the same time make a protest,” he said as cited by the public broadcaster NHK.

Japanese officials including Prime Minister Shinzo Abe expressed outrage over the latest in a string of crimes, which has been poisoning US-Japanese military ties for decades. The country’s Foreign Ministry filed a formal complaint over the case as well.

Critics of the deployment of US troops in Japan complain of the crimes committed by American personnel against local residents, environmental damage done by US bases and other negative sides. Okinawa Island hosts roughly half of all American troops in Japan, and sentiment against the arrangement are especially strong there.

The Japanese government has invalidated Okinawa governor’s decision to revoke his predecessor’s approval of the relocation of a US military base within the prefecture, Japanese Land and Infrastructure Minister Keiichi Ishii said Tuesday.

Earlier this month, Okinawa governor Takeshi Onaga, who wants the base to be moved outside the region, sent an official nullification of the relocation approval to the Japanese Defense Ministry.

Construction plans for the relocation of Marine Corps Air Station (MCAS) Futenma from Okinawa's highly-populated district in the city of Ginowan to the Henoko region in the coastal area of Nago, triggered protests over environmental concerns and opposition to the US military presence in Japan.

In April, Japanese Defense Minister Gen Nakatani and his US counterpart Ashton Carter reaffirmed the relocation plan, as part of a 2006 intergovernmental agreement to realign the US military presence in the country.

Tokyo will resume construction work at the new site within the prefecture while the Okinawa Prefectural Government intends to challenge the central government's decision to court.

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.

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.

The governor of Japan's Okinawa prefecture said on Monday he will move to halt work on a contentious U.S.A. air base, a headache for Prime Minister Shinzo Abe at a crucial time in his push to get widely opposed security bills passed.

The central government wants to move the U.S. Marines' Futenma base to another location on the southern island, but many Okinawa residents who resent U.S. military installations want to get rid of it altogether.

Okinawa governor Takeshi Onaga, who won election last year on his anti-base stand and has accused Abe of looking down on the island, said his government will revoke a permit for key landfill work that is needed to relocate the base.

The government forced the bills through the lower house of parliament in July despite massive protests. More than half of people polled on the issue oppose the bills, which would allow Japan's armed forces to defend an ally under attack, a drastic shift in Japan's post-war security policy.

Okinawa, which hosts 75 percent of US military bases in Japan, is balking at plans for another base.

Once the independent kingdom of Ryukyu, Okinawa, was annexed by Japan in 1872. At the end of World War II, exactly 70 years ago, Okinawa was the site of one of the war's most ferocious battles. Caught between the armies of Japan and the United States, Okinawans suffered unspeakable horrors during the "typhoon of steel." Viewed as expendable under imperial Japan, many Okinawans were killed outright by Japanese soldiers or forced to commit mass suicide. An estimated 120,000 Okinawans - between one-third and one-quarter of the population - died between March and June 1945.

The pain inflicted during the war and its aftermath underscored the Okinawan core value nuchi du takara ("life is precious") and left many Okinawans highly adverse to warfare and militarism. Despite this, Okinawa has remained one of the most militarized places in the world for more than 70 years, first under direct US military occupation and continuing after Okinawa's "reversion" to Japan in 1972.

Okinawa is by far the smallest of Japan's 47 prefectures, and although it accounts for less than one percent of Japanese territory, it is home to around 24,000 US military personnel, almost half of Japan's total, and is burdened with nearly 75 percent of US bases in Japan.

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