The law approved last September initially required all students entering grades seven through 12 to get vaccinated by the start of the 2011-2012 school year. Lawmakers passed a 30-day extension this summer as districts worried many students wouldn't meet the deadline.
Under California law, students also can still attend if their parents file a form saying they oppose vaccines.
No statewide estimates of the number of students turned away is available because districts are not required to report their final vaccination tally until December, state education and public health officials said.
But anecdotal reports from individual districts indicate the percentage of students meeting the requirement varied widely, from about half of students to nearly all.
"We've done a tremendous amount of outreach with the schools trying to let them know," said Linda Davis-Alldritt, the school nurse consultant for the education department.
On Thursday, San Francisco Unified School District began sending home students who arrived without proof of vaccination or a parental personal belief exemption.
District spokeswoman Heidi Anderson said the district estimates about 2,000 students, or 10 percent of the student body, are still unvaccinated. The district held a free vaccination clinic at its offices Thursday and was providing shots at individual schools Friday.
District officials were optimistic that most students would be able to return to class soon.
"We're getting down to it," Anderson said.
The Folsom Cordova Unified School District hit the extended deadline Friday for having all students immunized. Mary Ann Delleney, director of health programs for the district, said about 2,250 students who have yet to get vaccinated won't be turned away.
"We will not withhold education for students, but we will make every effort that we possibly can to be in compliance with state law," she said. The district had 70 whooping cough cases last year, she said.
In the Natomas Unified School District in Sacramento, about 1,100 students hadn't received their immunization shots by Thursday night, said Janet Handley, the assistant supervisor of education services. The district's 30-day extended deadline ended Friday.
Students who show up Monday without proof of their immunization will be sent to the school's gymnasium for study hall, Handley said. The students who are sequestered into the gym will not count toward the district's attendance-based funding for those students on those days, she said. Schools in California lose money for each absence.
"We're trying to balance how to get the message out that they need to get the shot, and we also need them at school," Handley said.
Natomas High School hosted a free clinic after school Friday, where a line of students curled around the gym where nurses were administering shots. Many said they hadn't heard of the immunization requirement until this week, despite what health and education officials described as a barrage of information sent to parents, students and schools.
Jake Terry, a 12-year-old at NP3, a charter middle school in Sacramento, said he first heard about the shot requirement on the news.
"I'm scared about the needle's size," he said.
State education officials said allowing unvaccinated students on school premises at all broke state law, but that the education department had no power to sanction defiant districts.
Allowing unvaccinated students to come to school also puts the students themselves and others exempted from the vaccine for medical or personal reasons at greater risk, said John Talarico, chief of immunization for the California Department of Public Health.
"If one of them gets it and they're all together, you now have a whole pool of susceptible people," Talarico said.
San Diego Republican Assemblyman Nathan Fletcher, a co-author of the law, said students who haven't been vaccinated shouldn't be at school at all, regardless of the funding or instruction children might miss.
"This is not an academic or philosophical discussion. Children have died as a result of this. We took very seriously our obligation to protect children so I think school districts need to take seriously the obligations to comply with it," he said.
The vaccination mandate covers about 3 million public and private school students who public health officials say have lost much of their immunity since receiving their original immunization against whooping cough before entering kindergarten.
California saw more than 9,000 whooping cough cases diagnosed in 2010, the highest number in the state since 1947. Ten infants too young to receive the vaccine died from the illness. About 2,400 cases have been diagnosed so far in 2011, but the state has seen no fatalities.
The highest percentage of California students entered kindergarten last year in more than 30 years under a California law that allows parents to exempt their children from vaccines for philosophical or religious reasons, according to state health records. About 3 percent of incoming kindergartners received either a personal belief or medical exemption from state vaccine requirements.
Health officials said there was no firm link between lower vaccination rates and the rise in whooping cough cases. The vaccine's effectiveness also wears off over time and doesn't work for all people, Talarico said.