“It was my personal decision to come here,” Shindo told reporters, adding it was a “private” matter that should not affect Japan’s diplomatic relations.
Another cabinet member, Keiji Furuya, also made the trip.
“Consoling the souls of war dead is a 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 lawmakers visited the shrine for a spring festival, grabbing international headlines and sparking diplomatic protests.
On Tuesday, Seoul lashed out ahead of this week’s anniversary, saying “our government and people will never tolerate such visits”.
“We once again stress that there should be no trips by top Japanese politicians to the Yasukuni shrine,” South Korean foreign ministry spokesman Cho Tai-Young told reporters.
Even at home there is significant opposition to Yasukuni, including among some relatives of those honoured there, who say it glorifies war and the darker chapters in Japan’s history.
For many, however, walking down the shrine’s stone paths lined with cherry trees and past imposing gates dedicated to Shinto Japan’s animist religion is part of a ritual far removed from politics.
“My father held me only once before heading to the war zone knowing Japan would lose,” 69 year old Sumiko Iida told AFP Thursday.
“I’m absolutely against wars.”
Chinese state media on Wednesday reported Abe’s decision, relayed by the Japanese press and government sources, not to visit the “notorious” shrine.
Earlier in the week, the 35th anniversary of Japan and China normalising diplomatic relations passed quietly. Ties remain frosty following maritime skirmishes over a set of East China Sea islands that are disputed by both countries.
Observers have warned that the contested islands, which are believed to harbour mineral resources beneath their seabed, could be the flashpoint for military conflict between the two Asian giants.
Tokyo is locked in a separate territorial dispute with Seoul.
Abe has mostly focused his attention on reviving Japan’s economy since sweeping December elections, but he has also mulled changing the pacificist constitution imposed on Japan by the United States and its allies after the war.