He was recalled to Japan in October 1939 to assume the role of Vice-Minister of War in the cabinet of Prime Minister Fumimaro Konoe.

As the war conditions in the Pacific deteriorated for the Japanese, the Second Area Army was reassigned to the Southern Theater from November 1943, where Anami directed operations in western New Guinea and Halmahera.

[4] Even after the bombings of Hiroshima and Nagasaki, Anami opposed acceptance of the Potsdam Declaration and instead called for a large-scale battle to be fought on the Japanese mainland that would cause such massive Allied casualties that Japan would somehow be able to avoid complete surrender and perhaps even keep some of what it had conquered.

[5][page needed] Eventually, his arguments against what he perceived to be the dishonor of surrender were overcome when Emperor Hirohito ordered an end to the war.

[6] His refusal to support any action against the imperial decision was a key point in the failure of the Kyūjō incident, an attempted military coup d'état by junior officers to prevent the surrender announcement from being broadcast.

[4] On 14 August, Anami signed the surrender document with the rest of the cabinet and committed seppuku early the next morning.

His sword, blood-splattered dress uniform, and suicide note are on display at the Yūshūkan Museum, next to Yasukuni Shrine, in Tokyo.