"Nisei" received largely positive reviews. In a retrospective of the third season in "Entertainment Weekly", "Nisei" was rated an A. The review noted that the episode contained "lots of excitement for Scully", though it also described Mulder's plot thread as "equally gripping". Writing for "The A.V. Club", Emily VanDerWerff rated the episode an A-, calling it "a hell of a lot of fun". VanDerWerff described the cliffhanger ending as "just phenomenal", and felt that the episode had "the drive of a big-budget action film". However, she noted that it was becoming evident by this stage that the series' mythology was becoming "too big to ever resolve wholly satisfactorily". Paula Vitaris from "Cinefantastique" gave the episode a largely positive review and awarded it three-and-a-half stars out of four. Vitaris noted that, despite the teaser and first act being "promising enough", the episode "slides downhill rapidly with a storyline that crosses the border into ludicrous." Vitaris called the scene where soldiers kill prisoners "a scene more disturbing than anything else previously seen on "The X-Files"." Furthermore, she wrote that the final scene between Mulder and Scully was "beautifully written and acted."