Yoshitaka Shindo, Internal Affairs and Communications Minister in Abe's Cabinet, visited the shrine.
About 90 other MPs arrived at the site later in the morning.
"It was my personal decision to come here," Shindo said, adding it was a "private" matter that should not affect Japan's diplomatic relations.
Another Cabinet minister, Keiji Furuya, who is in charge of the North Korean abduction issue, also made the trip.
Tokyo is pressing North Korea to return all Japanese citizens kidnapped by Pyongyang in the past - the victims were largely used to train North Korean spies.
"Consoling the souls of war dead is purely a domestic issue," Furuya told reporters. "This is not something that other countries are supposed to criticise or interfere with."
Abe gave a ritual offering earlier this year when nearly 170 MPs visited the shrine for a spring festival, grabbing international headlines and sparking diplomatic protests.
On last year's surrender anniversary, more than 50 MPs made the pilgrimage to the site near Japan's Imperial Palace, drawing protests from Seoul and Beijing.
- AFP