DUBLIN — A tough new immigration law in Arizona has inspired Bay Area protests, boycotts and dinnertime debates, but a lesser-known federal program to deport illegal immigrants from county jails is likely to have a bigger local impact.

The fingerprints of every person booked at a county jail in the East Bay are now being immediately transmitted to Immigration and Customs Enforcement, a federal agency that uses the data to identify and deport illegal immigrants. The program, called Secure Communities, launched in Contra Costa County on April 6 and in Alameda County on April 20.

More than 5,300 fingerprints from East Bay inmates have been sent to immigration agents since early April, identifying nearly 90 noncitizen immigrants with some kind of criminal record, 16 of whom have been deported. The program also began in San Mateo County this week and in Solano and Sonoma counties this year.

Only in San Francisco, where the information-sharing program is set to roll out June 1, have local officials asked not to participate in the federal partnership, saying it will erode their relationships with immigrant communities. State Attorney General Jerry Brown denied that request Tuesday, arguing in a letter that the program "serves both public safety and the interest of justice."

The new system launched so quietly in the region's jails that many local officials this week said they knew nothing about it.

"This is something that is not on my radar scope," said Gayle Uilkema, a Contra Costa County supervisor from Lafayette and a Republican. "If people are talking about it, and are concerned about it, we need to be aware of it."

Contra Costa Sheriff Warren Rupf and his staff were not available to comment on the program this week.

San Francisco Sheriff Michael Hennessey wants to be able to opt out of the agreement that the immigration enforcement agency, known as ICE, made with the state Department of Justice last year. San Francisco supervisors were also scheduled to vote to opt out of the program Tuesday, though it remained unclear if they had the authority to do so.

"Sheriff Hennessey believes it's overbroad and he's concerned about the implications of that," said a spokeswoman, Eileen Hirst. "Secure Communities means every single person who is booked in our custody will be reported to ICE. That includes misdemeanors and people whose charges get dropped in the first few hours of incarceration."

That means tens of thousands of Bay Area residents could now be reported to ICE each year, regardless of the gravity of their charges. Hirst said that raises privacy concerns, creates a fear of reporting crimes and damages the relationship between law enforcement and the people it serves.

The federal program is now in place in at least 170 jurisdictions in 20 states, including 18 of California's 58 counties. Federal officials plan to have the entire country on the system by 2013.

Jailers in the state already take the fingerprints of incoming prisoners and forward the data to a state database, which is shared with the FBI. Immigration enforcement agents can now tap into the same stream of data. The state database includes people who submit fingerprints because their jobs require it.

"We just submit our prints like we always have," said Sgt. J.D. Nelson, spokesman for the Alameda County Sheriff's Office. "It doesn't impact us or our workload one way or another."

For some local jurisdictions, however, the program undermines a long-held pledge to not share information about undocumented residents with federal authorities. Local cities that describe themselves as sanctuaries for illegal immigrants include Oakland, Berkeley, San Francisco and Richmond. The four cities were among at least six in the Bay Area that passed resolutions this month criticizing or boycotting Arizona for its new law that makes illegal immigration a crime and encourages police to detain people suspected of being in the country illegally. At the same time, and unknown to many local officials, a little-known program was sending a growing number of Bay Area immigrants to federal detention centers.

Illegal immigrants arrested in East Bay cities and booked in a county jail are now, because of the Secure Communities program, far more likely to be flagged in the database and picked up by immigration agents than they were a few months ago. Immigration authorities put a hold on immigrants after being alerted that their fingerprints match a previous ICE record, and take custody of them after their local case is resolved. Previously, ICE agents visited local jails but checked inmates by their names, which is less reliable than their fingerprints.

Hirst, spokeswoman for the San Francisco sheriff, said her agency already forwards information about foreign-born felons to ICE. The sheriff delivered more than 3,100 inmates to ICE since 2007, according to a letter he recently sent to Brown.

"My department already has a system in place that reports individuals to ICE and I do not wish that it be replaced by Secure Communities," wrote Hennessey as he asked to opt out of the program, citing privacy concerns and the conflict with San Francisco's sanctuary ordinance. Hirst said city officials had no say in whether the federal program was implemented.

"There was no conversation. They just gave a date," she said.

Brown responded to the opt-out request Tuesday and defended ICE's program.

"In these matters, statewide uniformity makes sense," Brown wrote to Hennessey. "This is not simply a local issue."

Federal officials say the Secure Communities program is designed to remove illegal immigrants responsible for the worst crimes — Level 1 crimes such as murder, rape, kidnapping and robbery — but immigrant advocates say it casts too wide a net. About 22,000 illegal immigrants charged or convicted of a Level 1 offense have been identified through Secure Communities since October 2008, according to government statistics. Critics believe that is a fraction of the number of immigrants identified and deported through the program, and activist groups sued the government last month seeking more information.

"The program has been shrouded in secrecy since its inception in the final months of the Bush administration," said Chris Newman of the National Day Labor Organizing Network, one of the organizations suing for more information. "We'd like to know how the program goals were devised and how they will be measured."