"Until I receive the report, I cannot cooperate with U.S. nuclear submarines making port calls," Yohei Kono told reporters.
The 6,200-ton Chicago entered Sasebo port, 609 miles, southwest of Tokyo, on Monday, but U.S. military officials had only told the city government that it would stop outside the port, said city spokesman Keiichi Matsuda.
The submarine arrived from Pearl Harbor, Hawaii.
The 20-minute stop violated a 1964 bilateral accord requiring the United States to notify Japan 24 hours in advance of port calls for U.S. nuclear-powered submarines. The notice gives time for local authorities to check radioactivity levels in ports before and after U.S. submarine visits.
The U.S. Navy acknowledged the violation of the accord, attributing it to "an internal administrative error." But the Navy defended its safety record and said its ships pose no environmental hazards.
"U.S. Navy nuclear-powered ships have steamed more than 119 million miles and amassed more than 5,100 reactor-years operation without a reactor accident or any release of radioactivity that has had significant impact on the environment," the Navy said in a statement.
The port call has inflamed tensions between Japan and the U.S. military in the wake of a series of crimes linked to American bases here and the collision of a U.S. submarine and a Japanese fishing vessel off Hawaii that killed nine Japanese.
Sasebo City Mayor Akira Mitsutake called the Chicago's port call an "act of bad faith." It was the first port entry to violate the U.S.-Japan pact, he said.
Kono demanded an explanation.
"I have instructed my staff to ask the United States to clearly state why it defied previous practice and made a port call without prior notification and confirm the cause of the incident," Kono said.
Acting U.S. Ambassador Christopher LaFleur had told Japanese Foreign Ministry officials that the sub's incursion was caused by a miscommunication within the U.S. Navy, said a Foreign Ministry spokesman, who spoke on condition of anonymity.
The U.S. Embassy had no immediate comment.
Hideo Sawada, mayor of Yokosuka city, warned that the sub's unannounced port call could unnerve Japanese, particularly in cities that host U.S. troops.
Yokosuka, located 28 miles southwest of Tokyo, is the site of a U.S. Naval base. Sawada also said he planned to reiterate the necessity of U.S. forces to give 24-hour notice before port calls at Yokosuka.
Nearly 50,000 U.S. troops are stationed in Japan under a joint security treaty.
©MMI The Associated Press. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed