Japan's Prime Minister Shinzo Abe expressed "serious concern" over allegations the United States spied on senior Japanese government and business officials.
Abe also called for an investigation into the matter during a phone call with U.S. Vice President Joe Biden, said Yoshihide Suga, Japan's top government spokesman.
"If it is true these Japanese individuals were targeted, it could shake the relationship of trust in our alliance and I would have to express serious concerns," Suga quoted Abe as telling Biden.
Suga said Biden apologized for the matter, noting it has "stirred up debate in Japan." He did not say whether Biden specifically confirmed the spying.
Media whistleblower WikiLeaks last week published documents it says show the U.S. spied on 35 companies, government ministries and individuals in Japan.
Trade talks, climate change
WikiLeaks said the intercepts related to topics such as U.S.-Japan relations, trade negotiations and climate change strategy. It said the surveillance dates as far back as 2006, the first term of Prime Minister Abe.
In a statement late Tuesday, the White House said Biden used his phone call with Abe to reaffirm the United States' "strong commitment to the U.S.-Japan alliance and thanked Prime Minister Abe for his enduring partnership."
"The vice president reaffirmed the United States' commitment made by President Obama in a 2014 presidential directive to focus our intelligence collection on national security interests," the statement added.
It is the latest of several spying revelations that have strained relations between Washington and its allies.
In June, WikiLeaks released documents saying the United States spied on the last three French presidents, prompting a diplomatic dispute between the nations, despite friendly ties dating back to the 1700s.
In 2013, WikiLeaks reported that the U.S. National Security Agency had wiretapped German Chancellor Angela Merkel's private phone. The report sparked a political scandal in Germany and prompted an official inquiry.
The United States and Japan have been allies for more than a half-century following the end of World War II.