In the span of a weekend, two events have cast doubts on the durability of US deployments in Japan.

The first, obviously, is the alleged rape of a middle-school student by a thirty-eight-year-old Marine committed in Okinawa. The incident has prompted protests to the US consul-general and Marine commander in Okinawa, and promises on the part of US authorities to cooperate with local officials on the investigation and to work to ensure that this won’t happen again. The Foreign Ministry has also made demands to Joseph Donovan, US deputy chief of mission, to strengthen safeguards in Okinawa. Kishida Fumio, the minister responsible for Okinawa affairs, responded angrily, and called for stricter countermeasures.

The second was Iwakuni’s mayoral election. On the face of it, the election was good news for the US-Japan alliance and the Fukuda government, perhaps giving new life to the troubled 2006 realignment agreement that called for the relocation of US aircraft carrier aircraft from Atsugi in Kanagawa to Iwakuni. Fukuda Yoshihiko, the government-backed, pro-agreement candidate, defeated Ihara Katsusuke, the anti-base candidate, prompting government officials to celebrate Mr. Fukuda’s victory as a victory for the alliance. Ishiba Shigeru, defense minister, told reporters that he hopes to talk with the new mayor as soon as possible. “The US realignment,” he said, “must by all means be realized to maintain deterrent power and relieve the burden on communities.” Yomiuri, in its editorial on the election, echoed both lines of this argument, paying particular attention to the dangers of basing US aircraft at Atsugi in the Kanto plain.

The victory in Iwakuni, however, may be more illusory than the government’s celebratory response would suggest. Mr. Fukuda’s — or Messrs. Fukuda’s — victory was not quite a reversal of the 2006 referendum on realignment in which the citizens of Iwakuni rejected the plan to move the carrier aircraft (triggering the showdown with Tokyo over subsidies). In a Mainichi/TV Yamaguchi exit poll, a plurality (41%) said that they oppose the plan, and another 20% said that they oppose the plan, but believe that “it can’t be helped.” Only 2% approved the plan unconditionally, while 33% approve with conditions attached.

The campaign came down to economics — a plurality (31%) said that restoration of the city’s finances was the most important issue. A factor in the city’s finances, of course, is the government’s withholding funds to Iwakuni in response to its opposition to the relocation plan (the “stick” side of the government’s “carrot and stick” strategy).

Both events illustrate the corrosive impact the US presence has had on Japanese politics — and ultimately suggest that the alliance rests on a fragile political foundation. In order to see the agreement to its conclusion, Tokyo has subverted the will of local communities, a successful strategy thanks to fiscal centralization. The communities, not without reason, fear the consequences of hosting US forces, whether due to crimes committed by US personnel, the risk of plane crashes, and constant noise pollution. Is it appropriate for Tokyo to browbeat those communities into submission?

The Marine presence in Okinawa is particularly disruptive, given the greater impact of ground forces in local communities compared to naval and air enclaves.

The US and Japan need to rethink the feasibility of the basing arrangement. What manner of US presence is sustainable? What composition of forces in Japan will best enable the US to perform its East Asian missions?

As Richard Halloran argues in Air Force Magazine, the US will increasingly reorient its Pacific military assets to Guam, Hawaii, the West Coast of the US, with smaller facilities in Japan, Singapore, and elsewhere. Halloran quotes Admiral Timothy Keating, commander of US Pacific Command, as saying that the US will have fewer boots on the ground in the region by 2017. That makes the US naval base at Yokosuka, soon to be home to the nuclear-powered USS George Washington, the most important US military facility in Japan.

Every rape or assault by a Marine in Okinawa potentially undermines the US presence elsewhere in Japan — and the US should therefore consider unilaterally hastening the process whereby USMC personnel will be relocated to Guam. (This would entail an acceleration of the building process on Guam that has barely begun — but is that an impossible task?) As for the housing of US Navy carrier aircraft, if the planes are to be relocated to Iwakuni, the US Navy has to sell the move itself, much as the homeporting of the USS George Washington was sold to the people of Yokosuka. The US Navy must be a good neighbor, and must be receptive to local concerns, even if Tokyo isn’t.

Ultimately, though, the US footprint in Japan must and will shrink for the good of the alliance. Although Japanese hawks argue that US power depends on bases in Japan, US deterrent strength in the Western Pacific will be more durable once it’s located back on US territory, immune to the vicissitudes of Japanese public opinion.