Transport minister Chikage Ogi urged North Korea on Friday to let the families of Japanese abductees come to Japan aboard its ferry Mangyongbong-92.
The minister of land, infrastructure and transport made the remark while commenting on the departure of the North Korean ship from Niigata port earlier in the day.
The 9,672-ton passenger-cargo ship left the port without incident shortly after 10 a.m.
"Every time I see the ship enter port, I wish the abductees' families (who are living in North Korea) will return to Japan," Ogi told reporters. "It is regrettable that such human rights are not guaranteed to the abductees' families."
More than a dozen Japanese were abducted by North Korea in the 1970s and 1980s. Five of them returned to Japan last October, but they left behind their North Korean-born children and an American husband. Pyongyang has snubbed Tokyo's demands that the relatives be allowed to come to Japan.
Now that the Mangyongbong has a passing grade, it is exempt from Port State Control inspections for the next six months.
But Ogi said the ship and other North Korean vessels must be strictly checked by security authorities whenever they make port calls.