A federal judge ordered his immediate release late Tuesday and for him to stay in the United States to exhaust an application for permanent residency, which he had already begun.

Pablo Villavicencio, 35, an undocumented migrant, was detained on June 1 at the Fort Hamilton Army Base in Brooklyn, after a military policeman was not satisfied with his New York identity card and a background check confirmed that he was not a legal resident.

Immigration and Customs Enforcement were called and moved to deport him. He remained in custody until Tuesday when activists said he was back home with his family.

"Although he stayed in the United States unlawfully and is currently subject to a final order or removal, he has otherwise been a model citizen," Judge Paul Crotty wrote in the order.

"He now has two children, both of whom are United States citizens. He has no criminal history. He has paid his taxes. And he has worked diligently to provide for his family," he added.

The case sparked outrage among pro-immigration groups and Democrats, widening the gulf between the city and the federal government's determination to crack down on illegal immigration.

"The Villavicencio family has finally received a crucial measure of relief from their 53-day nightmare," said Adriene Holder of The Legal Aid Society.

"We will continue to fight alongside them to protect their right to remain in the community they call home," she added.

Villavicencio married his wife in 2013. Their daughters are age two and four.

Villavicencio entered the United States in 2008 and in 2010 ignored an order to leave voluntarily.

At a federal court hearing in Manhattan on Tuesday, Crotty had questioned the rationale for deportation, given Villavicencio's pending application for permanent residency.

"Is there any concept of justice here or are we just doing it because we want to?" Crotty asked. He later issued a written ruling, ordering the father's release from detention in New Jersey.

The Trump administration has sought to get tough on undocumented migrants, moving to deport even those without criminal records and with deep family ties to the United States.