"When it comes to the entry of U.S. submarines into Japanese ports, there is the established practice of the U.S. side giving 24 hours' prior notification before entry. So this case contravened that established practice," Foreign Ministry spokesman Norio Hattori said at a briefing Tuesday.
Foreign Minister Yohei Kono said earlier that the government would suspend cooperation with the U.S. Navy until it had received a proper explanation.
The USS Chicago called briefly at the port of Sasebo on Monday, apparently after a miscommunication between the submarine and land-based U.S. Navy personnel.
Since 1964, the U.S. has, by agreement, given Japan 24 hours' notice of the arrival of any nuclear submarine – to give the authorities time to check radioactivity levels before and after the visit. In Sasebo's case, 48 hours' notice is routinely given.
This week's incident is said to be the first time the agreement was flouted, although it was attributed by a government official to a "simple error" by the Navy.
The Kyodo news agency quoted an official as saying the submarine's crew told the Navy of its intention to enter the port, but Navy officials appeared to have mistaken the figures given for an anchorage outside the harbor mouth.
Sasebo officials had therefore been given the wrong information.
Politicians were reportedly angered. Sasebo is based in the Nagasaki region, where nuclear issues are sensitive. Nagasaki was one of two Japanese cities on which the U.S. dropped atomic bombs in 1945, bringing the Second World War to a rapid conclusion.
The presence of nearly 50,000 American service personnel in Japan has become an increasingly sensitive subject in recent months, after several crimes involving U.S. troops and the publication of undiplomatic remarks about Japanese officials, made in private correspondence by a senior officer in the U.S. Marines.
Matters came to a head with the collision in February of an American submarine and a Japanese fisheries training vessel off Hawaii. Nine Japanese died when the USS Greenville rammed the Ehime Maru during an emergency surfacing drill.
Kono conceded that Monday's port call was not comparable to the Ehime Maru sinking, but said the feelings of the residents of Sasebo and Nagasaki had nonetheless better be taken into account.
At Tuesday's press briefing, spokesman Hattori said as far as he knew, the Chicago had been engaged in "routine operations." Its visit was not thought to have had anything to do with the standoff between the U.S. and China over a midair collision involving a U.S. Navy surveillance aircraft and Chinese fighter planes.
China's refusal to allow U.S. officials immediate access to the crew of the American plane – which landed at a Chinese airbase after the incident – initially prompted the Pentagon to keep three U.S. destroyers in the area. They have since continued on their pre-assigned return voyage to the U.S. West Coast.
In an unrelated accident, it was reported that a U.S. F-16 fighter plane crashed into the sea off Japan during a routine training flight Tuesday. The pilot ejected safely, landed in the sea and was rescued from his life raft by a Japanese helicopter.
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