Japan's Cabinet approved an additional set of economic sanctions against North Korea on Friday, banning all North Korean imports and ships.
The ban is effective for six months from Saturday.
On Wednesday, a measure banning North Korean nationals from entering Japan took effect, two days after the North's claim of having successfully conducted a nuclear test.
Japan plans to discuss more countermeasures depending on Pyongyang's response, according to officials.
By the end of Saturday, North Korean ships currently harboured at Japanese ports will be requested to leave.
There were 22 North Korean ships in Japan as of Thursday evening at four ports in four prefectures - Otaru in Hokkaido, Maizuru in Kyoto, Sakai in Tottori, and Shimonoseki in Yamaguchi - according to the Land, Infrastructure and Transport Ministry.
North Korea has exported to Japan products such as vegetables and seafood, which amounted to 14.5 billion yen ($121.5 million) since 2005, according to media reports.
On Thursday, a senior North Korean diplomat said "strong measures" would be taken against Japan if additional sanctions are imposed in protest of Pyongyang's announcement of a nuclear test.
"We will take strong countermeasures," said Song II Ho, North Korea's ambassador in charge of diplomatic normalisation talks with Japan.
Japan had imposed sanctions against North Korea in July, shortly after Pyongyang test-fired seven missiles into the Sea of Japan.
Those measures included banning entry of the only ferry between the two nations as well as remittances to 15 institutions suspected of having relations with Pyongyang's nuclear programmes.