Between 1965 and 1985, a team of around 120 North Korean troops repeatedly abducted young Japanese fishermen, the conservative Sankei Shimbun reported, citing a government interview with a formerly high ranking North Korean military official.
The issue of Japanese kidnapped by North Korea is a running sore in relations between the two countries. Pyongyang admitted in 2002 its agents had snatched some young Japanese in what Tokyo said was an operation to train spies in Japanese language and customs.
Pyongyang insisted at the time that all the others had died. But suspicions persist in Japan that the isolated state has not come clean about the scope of its abductions and the issue colours all of Tokyo's dealings on North Korea.
Asked about the report, Keiji Furuya, the state minister in charge of the kidnap issue, declined to comment, saying he could not give specifics about what the government discovered.
The Sankei report today, which did not name the defector or say where the interview with him took place, comes as Japan has struck out alone to re-engage with North Korea.
Earlier this month a top aide to Prime Minister Shinzo Abe visited Pyongyang in a move that appeared to take Washington and Seoul by surprise.
But despite the keen threat felt by Tokyo, which lies within easy reach of North Korean weaponry, the kidnapping issue trumps all others because of its domestic resonance.