Sheriff’s departments in both Long Island counties said they no longer will hold in jail immigrants who are flagged for deportation unless federal officials produce warrants, curtailing participation in a controversial Immigration and Customs Enforcement program known as Secure Communities.

Suffolk County Sheriff Vincent F. DeMarco, in a memorandum last week to all personnel, said the agency “is NOT to hold an inmate solely on an ICE detainer” unless the federal agency presents his office with a warrant from a judge.

The Nassau County Sheriff’s Department said it altered its policy in June, requiring federal immigration officials to present at least “administrative warrants” before the agency will hold an inmate.

The switch from routine detention of immigrants in the country illegally who have been arrested puts Nassau and Suffolk among more than 200 jurisdictions nationwide, as tracked by advocates, that have withdrawn at least in part from the program. Since 2009, more than 369,000 immigrants have been deported or have voluntarily returned to their countries under Secure Communities.

Suffolk and Nassau had led the state, outside of New York City, for the number of immigrants expelled from the United States under the program, according to ICE figures.

As of July 31, ICE had sent 781 immigrants from Suffolk and 499 immigrants from Nassau back to their homelands since both counties joined the program in February 2011.

The local policy changes follow federal court decisions in Oregon and Pennsylvania cases where detention requests lodged by ICE were found to violate the constitutional right not to be held without probable cause and were deemed not to be mandatory, civil rights advocates and law enforcement officials said.

Secure Communities was set up as an information-sharing partnership between ICE and the FBI to identify what are described as “criminal aliens” through fingerprint checks. When an immigrant who has been arrested is flagged for potential deportation in the databases, either because of criminal history or immigration violations, ICE asks local jails to detain that person for its agents.

Lou Martinez, ICE’s spokesman with the New York field office, did not comment on the Long Island departments’ actions. In a statement, he said the agency “works cooperatively with law enforcement partners throughout New York as the agency seeks to enforce its priorities by identifying and removing convicted criminals and others who are public safety threats.”

Members of a coalition of advocacy groups that includes Make the Road New York, the New York Civil Liberties Union and the Long Island Civic Engagement Table hailed the changes, particularly in Suffolk, as a victory for immigrants.

The massive detention system violates American values, they said, and has fostered fear among immigrants and hindered cooperation with law enforcement.

“Holding on to someone for even a minute without a judicial warrant or a finding of probable cause that they have done something criminal is unconstitutional,” said Amol Sinha, director of the Suffolk Chapter of the New York Civil Liberties Union. “We had heard stories of people detained from two days to three weeks without any finding that they had done anything wrong, simply so that the federal government could investigate.”

It was not clear how many inmates have been released under the new rules, because the counties don’t keep track. DeMarco, in an interview, said 114 immigrants were among inmates at the county jail Friday who had been flagged for detention and would be released if no warrants were issued by federal magistrates or other judges.

DeMarco said he reached his decision after asking the Suffolk County attorney’s office to review the recent federal court cases. He described the change as a “good government” measure to comply with the law and protect taxpayers from lawsuits. Those charged with serious crimes still will be held under the terms of their cases, he said.

“I don’t want to open up the county taxpayers to any liability,” DeMarco said. “The bottom line is, the worst criminals out there, like those who commit murder or other violent offenses, won’t be let go by judges anyway. Serious crimes and violent felonies, those people are going upstate anyway.”

Michael R. Golio, a captain with the Nassau County Sheriff’s Department, said in a written statement that the agency “amended its procedures” on detention to require a warrant for arrest or deportation from ICE or the U.S. Department of Homeland Security.

“The Sheriff’s Department is aware of the recent federal court decisions issued in other states regarding this matter and we believe that our amended procedures are in full accord with the applicable legal authority on this issue,” Golio’s statement said.

Suffolk’s policy change “will not only prevent a torrent of unjustified deportation,” said Peter Markowitz, a law professor and head of the immigration justice clinic at Benjamin N. Cardozo School of Law in Manhattan, “but just as importantly will promote a healthy relationship between immigrant communities and Suffolk County law enforcement, and that’s going to make everyone safer.”

Markowitz and other advocates, however, were not convinced that Nassau’s change would make a difference, because the county will continue to accept administrative warrants, typically issued by ICE field office directors instead of a judge.

Barrett Psareas, an immigration enforcement proponent who is vice president of the Nassau County Civic Association, said he is concerned about the changes leading to fewer deportations.

“There’s a duty of every government to protect your people, and they are not protecting us if they are not holding these individuals who committed crimes,” Psareas said.

Immigrant advocates have maintained that many immigrants were caught in a deportation net after being arrested over minor offenses, and were turned over to immigration agents before being convicted of any crimes.

“This had to stop,” said Carlos Reyes, 37, a Central Islip resident and member of Make the Road New York. “The community was afraid, and what ended up happening was that in many cases people were deported and families were separated over insignificant incidents.”

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