Chief Cabinet Spokesman Yoshihide Suga told reporters that the two Japanese were both picked up in May, one in Zhejiang province and the other in Liaoning.
He refused to give details, including the specific allegations the two face. Japanese newspapers and television stations reported earlier that the two were both men.
One of the men was apprehended near military facilities in coastal Zhejiang and the second one near the border with North Korea at about the same time, according to the reports, which cited unnamed sources familiar with Japan-China affairs.