He could become the Willie Horton of the immigration crisis.

Milton Mateo Garcia, 28, was caught one year ago entering the U.S. illegally across the Mexican border and was deported back to his native Honduras.

But Mr. Garcia soon re-entered the U.S. illegally — federal authorities either don’t know how, or they won’t say. He settled with relatives in Philadelphia, where Mayor Michael Nutter had signed an executive order in April declaring it a “sanctuary city” for illegal immigrants.

Since then, it’s the city’s official policy to defy federal authorities seeking to deport illegal immigrants unless the person sought by the U.S. Immigration and Customs Enforcement agency has been convicted of a violent felony. More than 100 communities nationwide have enacted similar policies, with the tacit blessing of the Obama administration.

Living and working in sanctuary, Mr. Garcia last month, according to police, approached a 26-year-old Philadelphia doctor who was walking to her home in the city’s fashionable Rittenhouse Square neighborhood after a night out with friends. He is accused of forcing the woman into her apartment and raping her repeatedly.

Police said Mr. Garcia then stole the victim’s cellphone and rode away on his bicycle. In perhaps not the smartest of moves, Mr. Garcia kept the victim’s smartphone in his possession. Police said they found him, in part, by calling the phone and locating its signal.

With Mr. Garcia now in prison facing trial on rape, kidnapping and robbery charges, ICE has lodged a detainer against him, requesting that local police notify federal immigration authorities before he would be released. But Philadelphia police won’t honor that request unless Mr. Garcia is convicted of a violent felony and a judicial warrant is issued.

As with the case in the 1980s of Horton, a convicted felon whose additional crimes while on prison furlough provoked a political furor, Mr. Garcia’s situation highlights many of the criticisms of the administration’s handling of immigration — from encouraging illegal immigrants to make the journey to the U.S. to failing to secure the border and allowing a patchwork of sanctuary cities and counties where immigrants need not fear deportation.

“There’s some collective blame here,” said Jessica Vaughan, director of policy at the Center for Immigration Studies. “The city of Philadelphia has made itself a sanctuary and, in doing so, has been shielding lots of criminal aliens from deportation and creating an environment where people have no fear of immigration enforcement.”

She said the Obama administration also has encouraged leniency for illegal immigrants “by sending the message that local authorities are free to ignore their own agents when they try to remove these individuals.”

“There is no question that the Obama administration has encouraged cities like Philadelphia to adopt sanctuary and noncooperation policies that obstruct ICE from taking custody of offenders like this,” she said. “Earlier this year, senior ICE managers in [Washington] told local authorities explicitly that they are free to ignore local ICE officers when they issue detainers seeking custody of criminal aliens like Milton Mateo Garcia.”

Ms. Vaughan said this “creates conditions where criminal aliens are more likely to be released into the community and more likely to be able to victimize people when they could be sent home.”

She also said the administration’s policy of “catch-and-release,” in which captured illegal immigrants are released with a notice to appear at far-off court date, contributes to a breakdown in the system.

A spokeswoman for ICE, Gillian Christensen, wouldn’t address the question of whether Philadelphia’s sanctuary status played a role in Mr. Garcia’s case.

She did say that Mr. Garcia, also known as Milton Garcia-Vazquez, “was previously removed from the United States in June 2013” and that ICE has lodged a detainer against him since his arrest.

“By issuing a detainer, ICE requests that a law-enforcement agency notify ICE before releasing an individual in order to allow ICE to assume custody,” she said.

A spokesman for Mr. Nutter said the mayor still “fully supports his executive order” in spite of the Garcia case and believes it has enhanced public safety.

“At the heart of his concerns, and the core reason for his order, is his desire to create a stronger context in which all Philadelphians will feel able and willing to share information with the Philadelphia Police Department about public safety matters,” said Nutter spokesman Mark McDonald. “This policy will enhance public safety by reducing the fear held by some that interacting with the government, particularly on a criminal investigation, could result in a detainer for themselves or their loved ones.”

The head of New Sanctuary Movement of Philadelphia, an advocacy group that lobbied for the executive order, didn’t respond to a request for comment. The group celebrated the mayor’s move last spring.

“This is a huge victory for immigrants and their allies, who have fought for years,” the group said in a statement at the time. “Philadelphia now has one of the most progressive policies in the country!”

Homeland Security Secretary Jeh Johnson met in May with groups seeking stronger enforcement of immigration laws, and some participants said Mr. Johnson seemed frustrated with local governments defying ICE.

But while the president has jealously guarded immigration as a federal prerogative against states like Arizona that planned crackdowns, he hasn’t spoken out against or filed lawsuits to block “sanctuary” cities. Instead, he has urged congressional Republicans to approve comprehensive immigration reform that would create a pathway to citizenship for most illegal immigrants currently in the U.S.

In the current border crisis, White House aides say Mr. Obama wants to see the laws enforced.

“The president’s committed to enforcing the law,” said White House press secretary Josh Earnest. “The law will be rigorously applied.”

He added that the Senate bill, which House Republicans won’t consider, “would have a tangible impact on so many of the problems that we see in our immigration system, not just the problems that we’re seeing at the border.”

Republicans say that Mr. Obama’s nondeportation policies, plus other go-it-alone executive actions, mean they simply do not trust him to implement any security crackdown.

About 40,000 people annually re-enter the U.S. illegally after being caught trying to cross the border.

When he was arrested for the rape, Mr. Garcia was working at Tashan, an Indian restaurant in Philadelphia. The management said in a statement that Mr. Garcia had presented all required documents before he was hired as a part-time employee.

It’s unclear when Mr. Garcia returned to the U.S. after his deportation in June 2013, but apparently he came back quickly. Relatives told the Philadelphia Inquirer that he had been living in the city for about a year when he was arrested for the rape.

Conservative radio host Dom Giordano of Philadelphia wrote in the paper last week that the Obama and Nutter administrations share in the blame for the situation.

“If this alleged rapist [was] convicted, this woman would never have been raped if he was not here illegally,” he wrote. “And he would not be here illegally if our borders were not so porous; if restaurants would not look the other way and hire people here illegally; and if Nutter would not erect a neon sign welcoming illegals with his announcements that he would not aid federal authorities in enforcing our immigration laws.”

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