Government spokesman Yoshihide Suga said the decision was in response to North Korea's failure to provide a report on its investigation into abductions of Japanese decades ago.
Suga urged North Korea to promptly and honestly report its findings.
Japan bans North Korean-registered ships from entering its ports except for humanitarian reasons. It also bans chartered flights between the countries.
North Korea agreed in May 2014 during talks in Stockholm, Sweden, to reinvestigate the abductions in the 1970s and 1980s. It also promised a probe into all Japanese nationals living in North Korea. In exchange, Japan agreed to ease some sanctions, including restrictions on travel between the countries.
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