The administration has ordered agents to begin ignoring many of the illegal immigrants they encounter in prisons and jails, as President Obama begins to implement a lesser-known part of his deportation amnesty policy — though his program isn’t sitting well with either side of the immigration debate.

In a nod to so-called sanctuary cities, the president’s policy prohibits U.S. Immigration and Customs Enforcement agents from targeting most illegal immigrants for deportation, including most of those who come into contact with state and local police.

Agents can still troll jails and prisons, but are told to no longer go after illegal immigrants with offenses such as drug possession, theft or fraud if it involved stealing an identity to try to further their unlawful presences in the U.S., according to details of the policy released Tuesday by the House Judiciary Committee.

Even some illegal immigrants who are charged with serious felonies but are released by local authorities won’t be picked up by immigration agents until they are convicted, the committee said.

“President Obama is needlessly endangering our communities,” committee Chairman Bob Goodlatte, Virginia Republican, said in a statement announcing his findings on the program. “It’s past time for the Obama Administration to get its priorities straight and protect the American people instead of their political interests.”

Mr. Obama announced the policy as part of his Nov. 20 amnesty, but details of what the Homeland Security Department dubbed the Priority Enforcement Program are just emerging.

The program replaces Secure Communities, a George W. Bush-era program that the Obama administration embraced as a way to boost deportation numbers while focusing on criminals rather than on rank-and-file illegal immigrants who hadn’t had serious run-ins with the law.

Under Secure Communities, ICE agents and officers scoured prisons, jails and booking sheets for illegal immigrants they could deport.

Immigrant rights advocates argued that Secure Communities was poisoning relations between police and legal and illegal immigrants, making Hispanics in particular fear interactions with authorities and making them less likely to report crime altogether. That made them more susceptible to become victims, undercutting public safety goals, the advocates said.

They also said the administration was deporting illegal immigrants charged with or convicted of minor offenses such as traffic violations.

The advocates won victory after victory in city and county councils and even some state legislatures, as lawmakers passed legislation prohibiting police from honoring detainer requests from ICE, which asked local police to hold illegal immigrants for pickup.

Some federal courts ruled that the detainers weren’t binding because federal agents showed no probable cause, meaning immigrants were being detained in violation of their constitutional rights.

Mr. Obama bowed to the court rulings and political pressure. He scrapped Secure Communities in November and announced the replacement Priority Enforcement Program.

Under the program, agents will ignore many of the illegal immigrants they encounter and will change the type of cooperation they request from state and local police. Agents generally won’t ask a department to hold an immigrant who otherwise would be released, but instead will ask to be notified so they can be on hand for the release and have the immigrant transferred.

In limited instances, agents will still issue detainer requests, but will have to assert probable cause so police have a reason to detain people beyond their normal release dates.

“ICE will only seek transfer of individuals in state and local custody in specific, limited circumstances. ICE will only issue a detainer where an individual fits within DHS’s narrower enforcement priorities and ICE has probable cause that the individual is removable,” the agency said in a brochure describing the program. “In many cases, rather than issue a detainer, ICE will instead request notification (at least 48 hours, if possible) of when an individual is to be released. ICE will use this time to determine whether there is probable cause to conclude that the individual is removable.”

ICE Director Sarah R. Saldana told Congress last week that the program is winning converts among police departments that balked at Secure Communities. She said it’s better to cooperate with communities than to be adversaries.

“That’s what we’re working towards, and that’s how we got Los Angeles to say they’d cooperate with us, and Contra Costa as well in California, and we’re working with several other jurisdictions,” she said. “Always best to try to get people to come to the table to discuss matters than to force things down their throats.”

Ms. Saldana ran into trouble this year when she told Congress that she would welcome a law ordering sanctuary cities and counties to cooperate, saying it endangers public safety and her agents’ lives to have some of the illegal immigrant criminals released.

Hours later, after having been contacted by her superiors, Ms. Saldana retracted her statement, saying she didn’t believe it made sense to order locals to cooperate.

Immigrant rights advocates say the Priority Enforcement Program is still a problem because agents can issue detainers, even if they do it less often. The advocates warned that police who comply with the requests are still risking legal problems with the courts.

“PEP creates a trap for unwary local law enforcement agencies, which will be subject to legal liability should they choose to participate,” said Jessica Karp Bansal, litigation director for the National Day Laborer Organizing Network.

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