The de Blasio administration said on Tuesday that New York City would join a Justice Department program aimed at rooting out terrorist recruiting efforts in the nation’s cities, even though its tactics have raised concerns among some civil libertarians.

The decision to join the program, called the Strong Cities Network, had drawn scrutiny from American Muslim activists, the New York Civil Liberties Union and civil rights lawyers. More than a dozen groups urged Mayor Bill de Blasio, a Democrat, to reconsider New York’s participation, citing what they called an unfair focus on the activities of law-abiding American Muslims.

Aides to Mr. de Blasio spent days deliberating whether the city should take part. Ultimately, Mr. de Blasio decided to support the program at a United Nations forum on Tuesday, where the mayor spoke alongside the United States attorney general, Loretta E. Lynch.

Still, in his remarks, the mayor, who has promised to forge a more inclusive, tolerant New York, seemed aware of the concerns directed at his administration, and eager to rebut them. Speaking in soft tones, he described the Strong Cities program as fueled by “grass roots” efforts to be more tolerant of ethnic minorities. “When we undermine intolerance, we undermine extremism and violence,” Mr. de Blasio said.