The man, a student at Hokkaido University, had reportedly planned to fly to the Middle East this week to fight with the Islamic extremist group, which has cut a swathe through Syria and Iraq.
The student told police he "was planning to travel to Syria so as to join Islamic State to work as a fighter", the Mainichi Shimbun and other media reported.
He hatched the plan after spotting a job advertisement posted at a second-hand bookshop in Tokyo.
It said a monthly wage of 15,000 RMB (around USD 2,400) was payable for people "not afraid of violence" to work alongside Uighurs in Syria.
Uighurs are the mainly-Muslim inhabitants of China's northwest Xinjiang province. Beijing is facing mounting violence there, which it has blamed on separatists it says have been radicalized through contact with overseas-based terror groups.
Most scholars remain sceptical of China's claims, however, with some arguing that Beijing exaggerates the threat to justify its hardline measures in Xinjiang.
There have been no confirmed reports of Uighurs fighting alongside Islamic State in Syria or Iraq.
Hundreds of mostly young men have travelled from Europe and North America to join forces with the brutal group of jihadists, which has declared an Islamic "caliphate". However, this is believed to be the first attempt by a Japanese.
Japan has a tiny Muslim population, made up largely of relatively recent immigrants, and little history of home-grown religious extremism.
Detectives are also investigating the advertiser, the Yomiuri Shimbun said, without giving details of his or her identity.
The relationship between the bookstore and the advertiser was not immediately clear.
A police spokesman declined to comment on the case.
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