There is also a theory that he was forced to commit seppuku, not just because of his disorderly behaviours, but because of the close relation with the sonnojoi ha (supporters of the doctrine of restoring the emperor and expelling the barbarians) such as Mito Domain, Choshu Domain and Tosa Domain, because Niimi is enshrined in Kyoto Reizan Gokoku-jinja Shrine which was built to enshrine the tobakuha (anti-Bakufu, crushing-the-Bakufu faction) sonnojoi patriots in the Maiji period, though shinsengumi was the enemy of the tobakuha and Niimi was the leader.
明治になって倒幕派尊王攘夷志士を祀るためつくられた霊山護国神社に倒幕派の敵だったはずの新選組幹部である新見が祀られていることから、切腹は単純な乱暴狼藉ではなく水戸や長州藩、土佐藩などの尊王攘夷派との親密な関係があったからではないかという説もある。