The intercepts exposing US National Security Agency espionage follow other documents that showed spying on allies including Germany and France, straining relations with them.
Japan is one of Washington's key allies in the Asia-Pacific region and they regularly consult on defence, economic and trade issues.
"The reports demonstrate the depth of US surveillance of the Japanese government, indicating that intelligence was gathered and processed from numerous Japanese government ministries and offices," WikiLeaks said.
"The documents demonstrate intimate knowledge of internal Japanese deliberations" on trade issues, nuclear and climate change policy, and Tokyo's diplomatic relations with Washington, it said.
The group also pointed to intercepts about "sensitive climate change strategy" and the "content of a confidential prime ministerial briefing that took place at (Prime Minister) Shinzo Abe's official residence".
There is no specific mention of wiretapping Abe but senior politicians were targeted, including Trade Minister Yoichi Miyazawa, while Bank of Japan governor Haruhiko Kuroda was also in the sights of US intelligence, WikiLeaks said.
There was no immediate reaction from Tokyo. The claims of spying on trade officials come at a particularly sensitive time after high-profile talks kicked off this week in Hawaii aimed at hammering out a vast free-trade bloc encompassing 40 percent of the world's economy.
The United States, Japan, and 10 other Pacific Rim countries are looking to finalise the most ambitious trade deal in decades.
But Washington and Tokyo -- by far the biggest economies in the negotiations -- have sparred over auto sector access and Tokyo's bid to protect agricultural products from the proposed Trans-Pacific Partnership.
The spying goes back at least as far as Abe's brief first term, which began in 2006, WikiLeaks said. Abe swept to power again in late 2012.
The whistleblower group said four reports were classified as "Top Secret" while one was marked to indicate it could be released to allies Britain, Australia, Canada, and New Zealand.

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