The raid involved the home of a 55-year-old woman who investigators believe had conspired with another alleged agent, 59, who played a key role in the kidnapping, Japan's Kyodo News agency said.
The National Police Agency said earlier this month that they believe Ko Kyong Mi and her younger brother Ko Kang were snatched from their home in Saitama in 1973 by several colleagues of their father.
The agency suspect the father of being a North Korean agent believed to have been running a spy agency in Japan under the cover of a trading company.
Police suspect the children were held captive in Tokyo for about six months, then shipped to the North in 1974 on a spy boat from northern Japan.
North Korea admitted in 2002 that it kidnapped 13 Japanese citizens in the 1970s and 1980s.
Pyongyang sent five of them home later that year, but insisted the rest were dead.
Japan has demanded proof of the deaths, and says more of its citizens may have been taken.
It has refused to provide energy and economic aid to North Korea, as promised under a breakthrough nuclear disarmament agreement in February, or to normalise relations, unless progress is made on resolving the issue.