"I will withhold comment. But If this is true, as an ally, it's deeply regrettable," the government's top spokesman Yoshihide Suga told a regular press briefing.
Suga added that Tokyo was checking with the US on the Wikileaks report, issued Friday.
The latest WikiLeaks intercepts exposing US National Security Agency (NSA) activities follow other documents that revealed spying on allies including Germany and France, straining relations.
Japan is one of Washington's key allies in the Asia-Pacific region and the two countries regularly consult on defence, economic and trade issues.
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Claims that Washington spied on Japanese trade officials, among others, came just as delegates negotiating a vast free-trade agreement known as the Trans-Pacific Partnership failed to reach a final deal after several days of intense talks in Hawaii.
The US and Japan are the two biggest economies in the 12-nation negotiations, but they have sparred over key issues including auto sector access and opening up Japan's protected agricultural markets.
WikiLeaks said the US intercepts showed "intimate knowledge of internal Japanese deliberations" on trade issues, nuclear policy, and Tokyo's diplomatic relations with Washington.
Prime Minister Shinzo Abe did not appear to be a direct target of wiretapping but senior politicians were, including Trade Minister Yoichi Miyazawa. Bank of Japan governor Haruhiko Kuroda was also in the sights of US intelligence, WikiLeaks said.
The leaks come as Abe seeks to expand the role of Japan's military, a move applauded by Washington but deeply unpopular at home.