Japan has stepped up calls for further sanctions against North Korea since Pyongyang tested an intercontinental ballistic missile earlier this month in defiance of repeated UN resolutions.
The test has raised tensions in the region, pitting Washington, Tokyo and Seoul against China, Pyongyang's last remaining major ally.
Japan's move has added further acrimony to often fraught bilateral relations with China and drew a harsh response from Beijing.
Despite being major trading and investment partners they are frequently at odds over a maritime territorial dispute and lingering tensions over Japan's history of aggression in the first half of the 20th century.
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"It is important to strengthen pressure so that North Korea should act toward denuclearisation," Kishida told reporters.
"We will urge North Korea to take concrete action toward the resolution of issues," he said.
The Nikkei daily said among the five organisations are China's Bank of Dandong, a Chinese shipping firm and a North Korean trading house dealing with coal and other commodities
China immediately denounced the Japanese sanctions.
"We firmly oppose any other country to impose unilateral sanctions outside the framework of the UN Security Council and we especially oppose the sanctions targeted at Chinese enterprises and individuals," Lu Kang, spokesman for the Chinese foreign ministry, told a regular press briefing in Beijing.
"I would like to tell Japan that China will not accept the wrongdoing and will require Japan to withdraw this wrong decision," he said, warning the sanctions will "create major political hurdles for China-Japan relations".
China, which borders North Korea and is considered its only major ally, argues that negotiations are the best way to persuade Pyongyang to halt its nuclear and missile activities.
The Pentagon has picked up signs that North Korea is preparing for another missile test, a US defence official said earlier this week.
The official said the test would be of an intermediate- range missile or North Korea's ICBM -- known as a KN-20 or a Hwasong-14.
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