China and Japan have been taking steps for more than a year to improve relations that remain plagued by tensions over the legacy of World War II as well as a maritime dispute.
Ties, however, remain shaky and the Chinese allegations of spying by Japanese nationals have become a new irritant.
The arrests also come as China has detained people of other nationalities on security-related suspicions.
Yoshihide Suga, Japan's top government spokesman, said China informed Japan last month that a fourth Japanese had been formally arrested after being detained in Beijing in June.
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"The government is preparing to support (those citizens) properly through diplomatic offices overseas."
Few details have been released about the detained Japanese. Suga previously announced that three are men and one is a woman. All were apprehended last year, with news of the formal arrests coming in stages.
The arrests of the Japanese came after China in 2014 detained a Canadian missionary couple for alleged espionage.
China said Friday that it has charged one of the Canadians with spying and stealing state secrets.
Last month Swedish activist Peter Dahlin was held on suspicion of endangering national security, apparently caught up in a crackdown on human rights lawyers.
China passed a new "national security" law in July that was criticised by rights groups for the vague wording of its references to "security". This raised fears it could give police wide-ranging discretionary powers over civil society.