Japan's fisheries agency seized the boat, later saying the captain had refused to comply with an order to stop for an inspection.
China swiftly reacted, calling for Japan to respect the safety and rights of the Chinese crew.
The agency's first seizure of a Chinese vessel since 2022 comes three months after Japanese Prime Minister Sanae Takaichi ignited a diplomatic row over Taiwan.
Just weeks into her term, Takaichi said Japan would intervene militarily if Beijing sought to take the self-ruled island by force.
In response, Beijing summoned Tokyo's ambassador, warned Chinese citizens against visiting Japan and conducted joint air drills with Russia.
China also tightened controls on exports to Japan for items with potential military uses, fuelling worries that Beijing may choke supplies of vital rare-earth minerals.
The boat taken on Thursday was inside Japan's exclusive economic zone, 89.4 nautical miles (166 kilometres) south-southwest of Meshima island, Japan's statement said -- not a disputed area.
The captain, identified by the agency as Chinese national Zheng Nianli, 47, was released after China guaranteed payment of cash collateral, public broadcaster NHK and other local media reported.
Multiple calls by AFP to the fisheries agency went unanswered Saturday morning.
The 2010 arrest of another Chinese fishing boat captain off those islands in the East China Sea became a major diplomatic incident.
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