Secretary of State Debra Bowen said she would let counties use the machines in February's presidential primary if extra security precautions were taken.
Bowen said she made the decision in response to studies showing that the machines could be hacked.
Warren Slocum, San Mateo County's chief elections officer, couldn't be reached for comment Saturday, but according to past remarks, Bowen's decision is sure to disappoint Slocum.
In the hours before the Friday night decision was announced, Slocum expressed dissatisfaction with what little information he'd received about the pending decision. "It's been frustrating," he said.
In May he warned that any decision requiring a change in the electronic voting system would create havoc in the county's elections office.
Such short notice in advance of a crucial election "will create an impossible situation for any registrar, unless there are no changes required," Slocum wrote in a May 17 memo to the San Mateo County Board of Supervisors.
In 2006, the county purchased 2,100 eSlate voting machines, manufactured by Austin, Texas-based Hart InterCivic, for more than $10.4 million. It could have to shell out more to comply with the new security standards.
Bowen announced the measures minutes before midnight Friday, making good on a promise to tell counties at least six months before California's Feb. 5 presidential primary whether their voting equipment would be decertified.
The announcement leaves San Mateo County and other affected counties with little time to find alternate equipment, if needed, in time for the primary. The decision follows an eight-week security review of voting systems used in all but a few of California's 58 counties.
University of California computer experts found that voting machines sold by three companies Diebold Election Systems, Hart InterCivic and Sequoia Voting Systems were vulnerable to hackers and that voting results could be altered.
The review follows Bowen's campaign promise to investigate whether the state's voting systems are "secure, accurate, reliable and accountable." It included reviews of manufacturer and testing documentation, source-code analysis, testing for potential avenues for hampering or errors, and assessment of accessibility for a range of disabilities.
Bowen said she had decertified the machines, then recertified them on the condition they meet her new security standards. She also limited the Diebold and Sequoia machines to one per polling place. That will force some counties to find replacement equipment on a tight schedule.
The decision comes amid growing concerns nationally about the security and reliability of electronic voting machines. Three of the four largest voting machine companies were affected by the decision.
Bowen took her toughest action against touch-screen machines, in which a voter's ballot is generated by a computer. She said the machines made by Diebold Election Systems and Sequoia Voting Systems could be used only in early voting and to meet voting-access requirements for the disabled.
The model manufactured by Hart InterCivic can be used more broadly, she said. But all three systems can be used only under rigorous security procedures, including audits of the election results.
Bowen said optical-scanning systems, in which voters mark their choices on paper ballots that are then counted by computers, also were barred but re-certified under the new security procedures. Many critics of the voting machines favor the optical scanners.
In announcing her decisions late Friday night, Bowen said she also thought optical-scanning systems made it "easier for voters to see and understand" how their ballots were being tallied.
Voting-industry executives have been critical of how Bowen's office has handled a six-month review of the machines, and Sequoia issued a statement early Saturday expressing disappointment and insisting that its machines were safe.
Computer scientists from California universities, working at Bowen's request, recently released reports saying they had hacked into machines made by all three vendors and found several ways in which vote totals could be altered.
The scientists also said the software codes that ran the machines were susceptible to viruses that could alter vote totals.
Company officials have downplayed the results of Bowen's review, saying it reflected unrealistic, worst-case scenarios that would be counteracted by security measures taken by the companies and local election officials.
Those security precautions include surveillance cameras and log-in sheets, which limit access to the machines in most counties and could prevent hacking during an election.
Hart InterCivic issued a news release defending its equipment and promising to comply with Bowen's requirements.
Officials at Sequoia said they were disappointed with Bowen's withdrawal of the company's certification but would make necessary improvements. They said their equipment is accurate and secure.
A message left with Diebold early Saturday was not immediately returned.
Staff writers Suzanne Bohan and Rebekah Gordon contributed to this report.