The controversial Tokyo shrine honours millions of Japan's war dead, but also controversially includes several senior military and political figures convicted of war crimes.
An attached museum portrays Japan more as a victim of US aggression in WWII and makes scant reference to the extreme brutality of invading Imperial troops when they stormed through Asia.
Visits to the shrine by senior Japanese politicians routinely draw an angry reaction from Beijing and Seoul.
The visit came after two cabinet ministers paid homage on Sunday, while Prime Minister Shinzo Abe, a passionate supporter of the shrine, made a ritual offering on Saturday.
Abe himself is not expected to visit the shrine this time.
The conservative leader is due to hold talks next month with the leaders of China and South Korea, the countries that bore the brunt of Japanese military aggression in the 20th century.
Hidehisa Otsuji, a former health minister who led Tuesday's shrine visit, said he was not immediately aware whether any cabinet ministers or their representatives joined the group.
"With the (parliament) session being closed, the group was smaller this time. Still, we prayed and paid our sincere respects" at the shrine, Otsuji told a press conference after the visit.
He said he hoped Abe would visit the shinto sanctuary himself.
Abe has visited the shrine once during his time in office, in December 2013. That sparked anger among Japan's neighbours and a diplomatic slap on the wrist from the United States, which said it was "disappointed".
On Sunday, Sanae Takaichi, the internal affairs minister and a close associate of Abe, and Justice Minister Mitsuhide Iwaki visited the shrine.
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