Traveling to Hokkaidō, he became Navy Minister of the new Republic of Ezo, and while he took part in the Naval Battle of Miyako Bay and the Naval Battle of Hakodate Bay, the Ezo forces were defeated, and Arai was placed in prison, where he remained pending a sentence of death.
Ketika ia pergi ke Hokkaidō, ia menjadi Menteri Angkatan Laut Republik Ezo baru, dan ketika ia mengambil tempat dalam Pertempuran Angkatan Laut Teluk Miyako dan Pertempuran Angkatan Laut Teluk Hakodate, pasukan Ezo dikalahkan, dan Arai dimasukkan dalam penjara, dimana ia menunggu hukuman mati.