No charges have been filed so far and police have refused to provide further information.
One company, Nakano Corporation, a trading firm based in Tokyo, acknowledged it had shipped pumps to Taiwan and had been raided last week.
"I didn't know they went to North Korea until the police told me," Hiroshi Nakano, the company president, said.
According to the Yomiuri newspaper, the IAEA found evidence for the first time of Japanese machinery being used in the North Korea's nuclear programme last year.
The Japanese investigation focuses on a piece of machinery called a "sync pump" which the Yomiuri said can be used for separating uranium as part of the enrichment process for nuclear weapons.
Japan is one of five countries working to persuade North Korea to abandon its nuclear weapons programme in return for international aid.