A second vessel was also being searched for evidence of fishing in Irish waters. It is believed the Japanese, pursuing tuna, had laid monofilament lines linked to radio beacons and were waiting for monitoring to end. But Irish officers said surveillance would continue.
The Minato Maru was detained 20 miles inside Ireland's 200-mile fishery limit on Tuesday, reportedly with 8.5 tonnes of tuna in its hold and 60 miles of long-line equipment.
Irish surveillance crews on two armed vessels, with tracker-plane support, have also spotted more long-line gear in Irish waters. They think it does not belong to the first Japanese ship detained, but was left by sister ships in the same fleet lying just outside the Irish fisheries limit.
The long-line fishing technique is labour-intensive and involves leaving baited hooks at points along the line over a long distance. Tuna are migratory fish and are found where warm and cooler waters meet in the South Pacific and in the eastern Atlantic.
Irish fishermen say the latest case of apparent Japanese incursions underlines the pressure on Atlantic fish stocks. Conflict over tuna has led to disputes between Spanish and British fleets in recent years.
The Japanese ocean-going fleet roams thousands of miles around the world in search of tuna, until now relatively unexploited in Irish waters.
Efforts made by the Irish to break into the market are restricted by European Union netting regulations.
"We shall retain one of our ships in the area on a permanent basis," a spokesman for the Irish government said yesterday. "There will also be aircraft there on near-constant surveillance duty.
"It is an ongoing operation. We will not be going away until this is resolved."
If convicted of illegal fishing, the Japanese captains face big fines and the confiscation of their fishing gear by Irish courts.