Relations between the two nations have been marred by several irritants, including a maritime territorial dispute and lingering tensions over Tokyo's history of aggression in the first half of the 20th century.
China had already detained five other Japanese citizens since 2015, largely on suspicion of spying.
Four of them have been brought before criminal courts, according to the Asahi Shimbun daily.
Six other men - three in Shandong province and three in Hainan province - were detained in March, top government spokesman Yoshihide Suga told a regular press conference.
"We've been notified by the Chinese authorities that they violated domestic laws," he said, adding the government is "discussing the issue through our diplomatic missions abroad".
Suga did not answer when asked whether Tokyo had protested to Beijing over the issue.
In Beijing, Chinese foreign ministry spokeswoman Hua Chunying said the six were being investigated and Japanese consular officials had been notified.
"Chinese authorities have been investigating illegal activities," she said, declining to provide details and referring journalists to "competent authorities in China".
The latest detentions bring the number of Japanese held in China to 11, a foreign ministry official told AFP.
Japanese media speculated that the presence of military ports in both provinces may have caused them to be suspected of trying to access intelligence.
In recent years, Beijing has drafted a series of legislative measures including laws on national security, espionage and cyber-security.
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