As tensions intensify between Iran and Japan's key ally the United States, Abe has reportedly proposed serving as a go-between and is said to be weighing up a state visit to Iran.
According to the Mainichi Shimbun report, Abe's planned meeting with influential Khamenei will be the first such talks between a Japanese premier and Tehran's supreme leader.
US President Donald Trump said last week he remained open to talks with Tehran during his state visit to Tokyo, appearing to have given the green light to Abe's plan.
Abe considering Iran visit as early as mid-June
Abe will also meet Iran's president Hassan Rouhani before meeting Khamenei during his tour to Iran from June 12 to 14, the newspaper said, citing unnamed government sources.
Before Trump flew to Japan, the United States had announced it was sending 1,500 extra troops to the region, adding to the aircraft carrier group and nuclear-capable bomber planes already dispatched.
Trump himself threatened "the official end" of the country if Tehran ever attacked US interests.
But last Monday in Tokyo, Trump offered assurances that he can live with the Islamic republic's government, whose toppling has long been a dream for Washington hardliners.
"We're not looking for regime change," Trump said, explaining that he only cared about Iran not achieving nuclear power status.
Trump expects Japan's military to reinforce United States in Asia and beyond
"I do believe that Iran would like to talk, and if they'd like to talk, we'd like to talk also," Trump added, striking a relatively dovish tone on Iran.
Khamenei has likened negotiations with the Trump administration to "poison" since "they don't stand by anything", referring to Washington's withdrawal from the landmark 2015 nuclear deal signed by Tehran and world powers.
Japan and Iran have kept a good relationship as resource-poor Japan relies heavily on imports of oil from the Middle East, though crude from Iran accounted for just 5.3 per cent of the country's total imports last year.
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