Pyongyang's de facto embassy in Japan has slammed the arrest of the son of its director for alleged sanctions-busting trade with North Korea.

The suspect's arrest on Tuesday along with two other individuals represented a "reckless political crackdown (which) cannot be condoned," said Nam Sung U, vice head of the General Association of Korean Residents in Japan, also known as Chongryon.

Fifty-year-old Ho Jong Do, who also goes by the name of Masamichi Kyo, is the son of Chongryon head Ho Jong Man. He is among three people arrested for allegedly violating a unilateral Japanese ban on imports from North Korea in connection with a shipment of mushrooms grown there and brought to Japan for sale.

The North Korean regime itself voiced anger in the form of a commentary released by the official Korean Central News Agency on Wednesday. It called Japan's move an "unpardonable provocation" that will push relations between the two countries to "the worst phase."

Chongryon has functioned as North Korea's de facto embassy in Japan for decades in the absence of diplomatic relations between Tokyo and Pyongyang.

"The unreasonable arrests will have a serious impact on future (North) Korea-Japan relations for which the Japanese government will be fully responsible," Nam told a news conference.

The investigation centers on a shipment of mushrooms alleged to have originated in North Korea, which would constitute a breach of the economic sanctions Japan has maintained since 2006 over Pyongyang's missile and nuclear tests.

Police raided the residences of Ho and Nam in March in connection with the allegations.

The KCNA commentary held the Japanese government responsible for the arrests. Bilateral talks between Tokyo and Pyongyang resumed last year, but have foundered on the unresolved issue of North Korea's abductions of Japanese nationals in 1970s and 1980s.