On Thursday, instead of showing up at her immigration check-in with a nonstop ticket to Guatemala, as she had been told to do, Amanda Morales Guerra, 33, walked into Holyrood Episcopal Church-Iglesia Santa Cruz in Washington Heights. She did not know when she could emerge again.

Local clergy estimate that more than a dozen people around New York City have quietly been hiding in churches to avoid deportation from federal immigration agents since the Trump administration began, but Ms. Morales was the first to publicly seek sanctuary.

“Sincerely, I don’t want to abandon my children,” she said in Spanish, sitting on the floor of the rectory library, where she and her three young children would also sleep. “I’m doing it for them because I love them and I would die if something happened to me or my children.”

The United States Immigration and Customs Enforcement agency responded firmly on Friday morning. “She is now considered an ICE fugitive,” said Rachael Yong Yow, a spokeswoman for the New York field office.