Vaccination rates in California schools reached an all-time high last school year, but one subset of public schools still appears to be lagging behind: charter schools.

A KPCC analysis of recently-released state vaccination rate data shows students in charter schools are much less likely than their peers in traditional, district-run public schools to be up to date on all of the shots California law says they should receive by seventh grade.

That's not necessarily because charter schools — which are managed by non-profit entities and independent boards, not school districts — are openly flouting the rules. Many charter schools operate as virtual schools or "independent study" home school programs, meaning their students would be exempt from the state's immunization laws.

"A majority of charter schools operate like the regular public schools do — it’s ‘no shots, no school,’ and they’re very strict about it," said California Immunization Coalition executive director Catherine Martin.

"But," Martin added, "there are also some charter schools that I believe get the [immunization] records, but if they feel like they’ve gone as far as they can in requesting those records [from parents], then I think they let it go and they don’t follow up."

Overall, 98.4 percent of California's seventh graders met immunization requirements in the 2016-17 school year, a 1.8 percentage point increase over the last three years, according to data the state Department of Public Health released recently.

KPCC cross-referenced this database — which covers all public and private schools in California that serve the seventh grade — with the state Department of Education's school directories.

The analysis found that at least 95 percent of the seventh graders were fully "up-to-date" on their immunizations in 96.8 percent of district-run public schools — 1,762 out of the 1,820 district schools reporting data.

Fewer charter schools met that mark. In only 73.6 percent of charter schools were most seventh graders up-to-date on their shots — 372 out of the 505 charters reporting.

Kyle Stokes/KPCC

Some of this gap is to be expected. In 2015, California lawmakers passed Senate Bill 277, exempting students who don't receive "classroom-based instruction" from the state's immunization laws — from private homeschoolers to children enrolled in "independent study programs," a label that often includes virtual charter schools.

"There is a higher percentage of charter school students enrolled in independent study program than in the traditional system," noted Richard Garcia, a spokesman for the California Charter Schools Association, in an emailed statement. (State data show there are 101 charter schools offering instruction either primarily or entirely online.)

Senate Bill 277 also carved out another new exemption, specifying that any student receiving special education services must continue to receive all services spelled out in her individualized education plan, or "IEP," regardless of whether she is up-to-date on their shots.

However, the new law's latitude for special education students or students in independent study programs does not entirely explain the gap between charter and district schools, KPCC's analysis shows.

Most seventh graders in 98.1 percent of traditional public schools were either up-to-date on their immunizations or fell subject to one of Senate Bill 277's special education or independent study provisions.

Again, that number was lower in charter schools: in only 85.4 percent of charter schools did most students meet those same conditions.

One possible explanation for the gap has to do with another exemption available under the state's immunization law.

Senate Bill 277 ended the "personal belief exemption," which allowed parents to choose not to vaccinate their children for religious or other reasons. This provision was controversial, riling opponents of mandatory vaccination and prompting legal challenges to the state's immunization law.

But physicians can still issue a "permanent medical exemption," documenting a "physical condition or medical circumstances" that should excuse a student from receiving one or all of the state-mandated immunizations.

The percentages of permanent medical exemptions issued, while minuscule in the grander scheme, did increase substantially during the 2016-17 year, according to the state's newly-released seventh grade data.

KPCC's analysis found that in almost all traditional, district-run public schools, between 0 and 10 percent of seventh graders received permanent medical exemptions. Only three out of 1820 district-run schools reporting data were exceptions to this rule.

Charter schools were a different story. KPCC found 24 out of 505 charter schools reported permanent medical exemption rates higher than 10 percent. At one virtual charter school based in San Diego County, 57 percent of seventh graders received a doctor's note excusing the student from vaccination, the state data show.

The California Immunization Coalition's Catherine Martin suspects some charter schools are attracting the type of parent who, as she put it, "may have more resources to seek a medical exemption with a physician that is more — I think the nice way to put it is, more flexible about their review of immunization status."

"Basically," Martin said, "they may have resources to pay a physician to provide them with the medical exemption that they seek."

Martin said her organization — a non-profit that represents a spectrum of a health care companies and professionals in its touting of vaccine awareness — has similar concerns about private schools. Most private schools are required to follow the law, but often don't report their immunization data.

More than 433 private schools did not report data this year — about 37 percent of all private schools with seventh graders. Around 10 percent of charters — 55 schools — did not report data. Less than 3 percent of district-run schools did not report data.

Garcia said the California Charter Schools Association, a membership organization that advocates for and offers help and guidance to charter schools, provides its constituent schools "with information related to requirements and the options for vaccinations."

"Charter public schools are not exempt from immunization requirements," Garcia said, "and continue to work with parents by providing education in order for students to be compliant."

This story has been updated to add the chart.