“Our credibility is at stake with the immigrant communities that we work with,” said Manny Castro, executive director of New Immigrant Community Empowerment, which works with day laborers in Queens.

He added: “If something were to happen with this data that led to a family getting detained or deported, then how are immigrants supposed to believe the city when it comes to providing information to the police or public schools? It took decades for the city to build this credibility.”

The IDs have also been popular with some of New York’s most vulnerable residents: those living in homeless shelters, victims of domestic violence and transgender people. The cards allow entry to public schools, are accepted by the Police Department as a form of identification for people reporting crimes and grant free admission to museums.

According to the city, more than half of cardholders use the IDs as their primary form of identification. Since the program’s inception and somewhat rocky start, the city has issued 988,066 cards.

The application does not ask applicants their immigration status. To obtain a card, an applicant can, for example, use a valid foreign passport or a consular identification, along with a utility bill that verifies a city address. An expired foreign passport is acceptable for up to three years, but the applicant may require two additional forms of proof. In addition, proof of residency in a homeless shelter for 15 days can be a form of identification.

Mr. Castorina said he became alarmed in September when New York State’s banking superintendent encouraged all state-licensed banks and credit unions to accept IDNYC. Only 13 banks in New York City accept the ID, and the de Blasio administration had pushed the superintendent to make such a recommendation to expand access to financial services for undocumented immigrants.