They were Tokyo’s worst-kept diplomatic secrets: clandestine cold war era agreements with Washington that obligated Japan to shoulder the costs of United States bases and allow nuclear-armed American ships to sail into Japanese ports.

For decades, Japanese leaders have gone to great lengths to deny the pacts’ existence, despite mounting proof to the contrary from the testimony of former diplomats and declassified documents in the United States. The most sensational instance came in 1972, when a reporter who unearthed evidence of one of the treaties was arrested on charges of obtaining state secrets, reportedly by means of an adulterous affair.

Now, the so-called secret treaties are causing problems again, this time in how Japan is handling its suddenly rocky relationship with the United States.

The new administration in Tokyo, whose election last summer ended a half-century of nearly unbroken control by the Liberal Democrats, wants to expose the treaties as a showcase of its determination to sweep aside the nation’s secretive, bureaucrat-dominated postwar order. Last fall, the foreign minister appointed a team of scholars to scour Japanese diplomatic archives for evidence of the treaties. Its findings are due this month....