The newspaper added China appeared to be looking into whether the men were acting under instructions from the Japanese government.
"We are aware of the reports but would like to refrain for commenting on specific incidents," Chief Cabinet Secretary Yoshihide Suga told a regular news conference.
"Our country in every case is making every effort concerning the safety of our citizens overseas."
Asked if Japan was involved in any spying against China, Suga again declined comment on any specific cases but added: "Our country is certainly not doing such things. I would like to say that this is the same with regard to all countries."
Chinese President Xi Jinping has overseen a tightening of already strict security laws and regulations, including setting up a new national security commission and renaming the national security law, which took effect in 1993, as the Counterespionage Law.
In 2010, four Japanese nationals were temporarily detained in China on suspicion of entering a military zone and taking photographs without permission. The detentions came at a time of escalating tensions between Tokyo and Beijing.
Sino-Japanese relations, coloured by Japan`s occupation of parts of China before and during World War Two, have thawed since Prime Minister Shinzo Abe met Xi twice since last November.
More about:
