San Francisco police officers handcuffed a car-theft victim, ran his name for warrants and then released him into the waiting arms of federal immigration agents, records show, in what is being investigated as a possible breach of local sanctuary-city laws.

Pedro Figueroa-Zarceno, 31, was released from jail Wednesday after two months and spoke at a news conference Friday. Afterward, Police Chief Greg Suhr acknowledged that the longtime city resident never should have ended up in the custody of immigration agents.

Police officials did not specifically admit to calling those agents, but federal officials said police had done just that.

“We are happy and relieved that Mr. Figueroa-Zarceno has been restored to his family,” said Sgt. Michael Andraychak, a police spokesman, in a statement.

“It is the policy of the San Francisco Police Department to foster trust and cooperation with all people of the city and to encourage them to communicate with SFPD officers without fear of inquiry regarding their immigration status,” Andraychak said. “We are aware of concerns this incident has raised with some members of our community.”

He said the police force had opened an internal affairs investigation to determine whether any officers should be disciplined.

Deportation order

The incident raised questions about how San Francisco authorities interact with immigration agents. The controversy flared last year after the Pier 14 killing of Kathryn Steinle by a Mexican national who was facing deportation but had been freed from San Francisco jail under the sanctuary-city laws.

Federal officials said Figueroa-Zarceno was the subject of a deportation order arising from his failure to appear at an immigration hearing in San Antonio in December 2005, and from a 2012 conviction for drunken driving.

But Figueroa-Zarceno’s attorney and San Francisco Supervisor John Avalos said the police cooperation with immigration authorities violated the city’s sanctuary-city ordinance that bars any use of money or resources to “assist in the enforcement of federal immigration law” — an ordinance designed in part to make potential crime victims and witnesses feel comfortable working with authorities regardless of their immigration status.

As San Francisco officials work to clarify policies in the wake of the Pier 14 case, immigration advocates say Figueroa-Zarceno’s detention is an example of a broken immigration system — and yet another reason why San Francisco needs to strengthen its policies.

Make policy ‘stronger’

“We want to make sure that as the sanctuary policy is politicized by what’s happening on a national level, that we can protect it and make it stronger and make sure that people like Pedro do not get impacted,” Avalos said.

Figueroa-Zarceno, a Mission District resident, had reported his car stolen in November. Then, on Dec. 2, he received word from the police that they had found it. But when he went to the Southern Police Station on Third Street to get the police report, he said he found himself in handcuffs.

According to a report from the U.S. Department of Homeland Security, which oversees immigration, San Francisco police ran a routine background check on Figueroa-Zarceno and discovered that he had an outstanding warrant out for his deportation from more than 10 years ago.

Eileen Hirst, chief of staff for the San Francisco Sheriff’s Department, said police officers contacted her department’s central warrant bureau, whose job it is to confirm warrants.

She said deputies contacted the service center at the U.S. Immigration and Customs Enforcement and confirmed the warrant. The deputies relayed the information to police, who had authority to decide whether to honor the warrant, Hirst said. The Homeland Security report said an ICE duty officer was informed of Figueroa-Zarceno’s whereabouts by both the service center and San Francisco police.

Back at the station, “I was handcuffed because they told me there were questions they needed to ask me, but there were no questions asked — I was simply handcuffed for about 15 minutes,” Figueroa-Zarceno said Friday.

ICE was waiting

“I was happy that they told me they were going to release me,” he said, “but once I got out of the Police Department, there was ICE outside.”

As his 8-year-old daughter screamed, “Papi! Papi!” and begged federal agents not to take him, Figueroa-Zarceno was shackled, put in a van and driven to a Contra Costa County jail where ICE houses inmates. He was released Wednesday on bail.

ICE officials said Friday that Figueroa-Zarceno is one of the “at-large foreign nationals who meet the agency’s enforcement priorities, including convicted criminals and other individuals who pose a potential threat to public safety.”

“Mr. Zarceno-Figueroa’s case is now being reviewed by the immigration courts to determine whether he has a legal basis to remain in the U.S.,” said James Schwab, an ICE spokesman, in a written statement.

Figueroa-Zarceno says he never defied immigration authorities. He came into contact with ICE shortly after he entered the country and explained he planned to file for asylum from the violence in El Salvador, said his attorney, Zachary Nightingale.

Aunt in San Francisco

He told the agents he planned to go to San Francisco, where his aunt lived, but still intended to go through the hearing process, Nightingale said. He said his client provided his aunt’s address in San Francisco, but never heard from authorities.

“That is not uncommon in my practice to see people whose cases go off the rails for reasons that are not their fault,” Nightingale said. “To me, this clearly indicates why San Francisco should not just be turning people over blindly to ICE.”

The question of whether notifying ICE of a person’s immigration status constitutes a violation of sanctuary-city laws was fiercely debated following the Pier 14 killing. A month before the suspect in that case was released, then-Sheriff Ross Mirkarimi issued a memo banning all communication with immigration agents seeking to deport jailed suspects, absent a warrant or court order.

New sheriff, new view

Newly elected Sheriff Vicki Hennessy is working to reverse that order to allow for some cooperation with federal agents in the most serious criminal cases, a move that has been criticized by advocates for immigrants.

Christine Falvey, a spokeswoman for Mayor Ed Lee, said Friday that the mayor remains “a firm supporter of the sanctuary-city policies.” After Suhr alerted him of Figueroa-Zarceno’s case, the mayor reached out to the Homeland Security secretary, she said.

“He expects the chief to fully review this case to make sure this doesn’t happen again, and the chief has assured a thorough review will happen as soon as possible,” Falvey said.

Vivian Ho is a San Francisco Chronicle staff writer. E-mail: vho@sfchronicle.com Twitter: @VivianHo