Illegal immigrants will have a harder time securing a job — some jobs, at least — as more Bay Area employers screen new hires through an immigration records check.

From corporate giants Apple (AAPL) and Chevron to the organic-friendly grocer Berkeley Bowl and the nonprofit Kaiser Permanente health care organization, more than 26,000 employers in the state have signed up for the federal E-Verify program that checks the immigration status of employees.

As a growing number of states require public and private employers to use E-Verify, California has gone out of its way to make it voluntary, passing a law this month that bans local governments from forcing firms to use electronic verification.

Still, the number of California job sites using E-Verify to scrutinize their workers — usually on the first few days on the job — increased by 37 percent to more than 90,000 from a year ago, according to government records. The state has more job sites using the electronic verification system than any other.

Some firms voluntarily run their employees through the E-Verify database in hopes of avoiding government audits or immigration raids that could lead to fines or damage their brands. Federal contractors participate because they must. When E-Verify flags work documents as suspicious, employees can challenge the Department of Homeland Security or quit. About 2.5 million workers in California had their paperwork audited through the system in the past year.

Retailers have been particularly eager to join in recent months, said attorney Ann Cun, of San Ramon-based workplace consultants INSZoom. That could affect who gets hired as stores and warehouses prepare for the annual surge of temporary work over the holidays.

A Target store in Walnut Creek made news just before Christmas 2009 when an internal audit forced out 40 immigrant workers on the overnight shift.

Immigration agents have conducted their own investigations of companies across the state — usually in low-key visits to audit I-9 forms and occasionally in a splashy public raid. All these probes make businesses worried.

“Employers have been finding out about the E-Verify program mainly after reading about these raids,” Cun said. “That’s usually what triggers companies to evaluate whether they want to enroll.”

Bad for agriculture?

For all the companies in the state joining E-Verify, however, hundreds of thousands have not, and agriculture is among the least represented industries, according to a list of E-Verify users obtained by this newspaper.

“There is one industry that I believe has historically shown it relies on foreign labor, and that’s agriculture,” said U.S. Rep. Dan Lungren, R-Gold River.

The Central Valley lawmaker reflects the mixed feelings many Californians have about E-Verify. Eighteen other states have made E-Verify use a requirement for some or all employers. California did the opposite this month, banning itself and local jurisdictions from mandating the program. The bill by Assemblyman Paul Fong, D-Cupertino, which takes effect Jan. 1, was backed by immigrant advocates but also the California Chamber of Commerce and agriculture groups.

“Overall, for the companies that have chosen to voluntarily participate, it’s worked very, very well,” Lungren said of E-Verify. “It’s not a fail-safe system, but it’s miles ahead of everything else.”

However, forcing E-Verify on all employers would devastate California’s agricultural economy if the mandate is not coupled with another source of farm labor, Lungren said.

“You’re going to destroy agriculture in a very real sense,” he said. “I don’t think I’m being an alarmist about that.”

E-Verify politics

E-Verify is emerging as a hot topic ahead of the 2012 presidential election, but perspectives do not always fall along simple party lines.

Proponents say enacting E-Verify everywhere could deter illegal immigration more effectively than any border wall by denying all jobs to illegal immigrants.

Republican presidential candidate Mitt Romney has made mandatory E-Verify a key talking point on the campaign trail, and the House Judiciary Committee has already approved a bill — the Legal Workforce Act — that would make the electronic system mandatory and replace I-9 forms. Most Democrats oppose the bill.

Among E-Verify’s most vocal opponents are business interests, immigrant advocates and some tea party libertarians who believe the system is too intrusive.

“There’s a lot of uncertainty,” said Cun, expressing concerns she said businesses have raised. “All this data is collected as you’re punching it in. What’s going to happen to all that data in five years? We don’t know.”

The U.S. Government Accountability Office said errors persist in the way E-Verify works. The process misses some illegal immigrants and misidentifies some authorized workers. Because it has a hard time picking up identity fraud, it may miss about half of all undocumented workers, according to a report produced for the Department of Homeland Security.

Economic impact

Opponents also point to places such as Alabama, where farmers blame new immigration restrictions for scaring away workers they depend on. A study released this month compared sanctuary cities that left illegal immigrants alone with those, such as California’s Lancaster, that mandated E-Verify use locally.

“Those who are proponents of restrictive ordinances would say, ‘That’s exactly what we’re trying to do.’ But we’re not looking just at the effect on immigrants,” said Jason Marczak, policy director for the Americas Society/Council of the Americas. “We’re looking at the overall effect on the number of jobs, the number of employees and the city as a whole.”

“Restrictive ordinances are bad for business, and nonrestrictive ordinances are comparatively better for the business environment,” Marczak said.

Lungren said he would support E-Verify across the country if Congress also passed a better guest-worker program that would bring in seasonal farm labor. A guest-worker program already exists, but Lungren said it is ineffective for most farm employers and last month he introduced a bill for a new guest worker visa that would allow foreign workers to stay for up to 10 months and would not require employers to house them.

Early adopters

Not all food-related businesses have resisted E-Verify. Among the earliest adopters was the meatpacking and processing industry, which experimented with electronic verification in the late 1990s, before it was called E-Verify.

“When you’re in that kind of industry, whether it’s clothing-making or animal-processing, you get a lot of illegal immigrants trying to get those jobs,” said Jeremy Russell, spokesman for the Oakland-based National Meat Association. “It’s easier for ICE to target us for raids. You have a big factory.”

Fear of raids put meatpacking plants at the forefront of electronic verification. “It’s easier for ICE to target us for raids. You have a big factory,” Russell said.

But it also created a false sense of security, Russell said. One early adopter, Swift & Co., was raided in six states in 2006, in part because E-Verify was not flagging the workers who used stolen Social Security numbers.

“That raid really put it on the map for everybody. You can’t just turn on E-Verify and say everything’s fine,” Russell said.

Database editor Daniel Willis contributed to this report.