Millions of Americans have apparently skipped their second COVID-19 vaccine doses, but exactly how many in California did so remains unclear, partly because the state’s disjointed vaccination system makes it difficult to track people who go to different clinics for their two individual doses.

According to data obtained by the New York Times from the Centers of Disease Control, more than 5 million people — or nearly 8% of those who received a first dose of the Pfizer or Moderna vaccines — have missed their second shots as of April 9.

Public health experts suggest the reasons for that may range from fear of the pain and illness some people have felt after getting second shots to the hassle of taking time off work or arranging transportation for another dose.

Some vaccine providers, such as Kaiser Permanente, canceled second-dose appointments earlier on in the vaccination effort because they ran low on supply, requiring patients to reschedule.

The trend is troubling to epidemiologists and public health officials who say evidence indicates a one-dose regimen can lead to a shorter term of protection, a weaker immune response and a bigger risk of getting dangerous variants of the coronavirus.

“It is certainly possible that people will have some level of protection after just one dose, but particularly with new variants circulating and without knowing how long that protection will last, those of us generally agree that people should get two doses with the appropriate interval in between in order to maximize their immediate protection and give them longer-term protection,” said Dr. Arthur Reingold, division head of epidemiology and biostatistics at UC Berkeley.

The California Department of Public Health is tracking the number of Californians who have missed their second doses but could not provide any numbers Tuesday because they’re “not readily available,” according to Sami Gallegos, spokesperson for the COVID-19 Vaccine Task Force.

Earlier data released by the CDC in March indicated that about 3.8% of Californians who got inoculated in the first few weeks of the nationwide vaccine campaign fell under that category.

But some people are raising questions about the accuracy of such data.

“It’s possible somebody went to one place to get their first shot and a different one for the second and those places weren’t talking to one another, recording two people as getting only one shot,” said Dr. George Rutherford, an infectious disease expert at UCSF. “I don’t know how big of a role that’s playing, but given how uncoordinated the process is, I think it very well may have skewed the numbers.”

Elizabeth Isabella, 44, of Burbank, also questions the numbers’ accuracy. In her case, she got her first shot at a walk-up clinic on April 6 in Bakersfield. When she realized she could get her second dose closer to home, she booked an appointment through the state’s MyTurn website but it made her schedule for two doses even though she needed just one more. As a result, the records would suggest she never got a second since she never returned to either clinic.

“I’m quite concerned that the system won’t register that properly,” she said. “And to the extent of vaccine passports and digital records, I’m worried that the paperwork and bureaucracy of it all will be a little screwed up.”

In most instances, a person is scheduled for a second-dose appointment at the same vaccine clinic where they received their first dose and reminder emails and messages are sent leading up to the second appointment.

But if someone misses a pre-scheduled second dose appointment, California’s largest health care providers and Bay Area public health departments are not tracking whether that person merely skipped the second dose or had secured a second shot elsewhere.

Sutter Health said in a statement this week that unless conveyed by a patient, it “does not currently have a way to know if they received their second dose outside our system. We expect that in time we will have this data from the (California Immunization Registry) database.”

Noel Sanchez, a spokesperson for the San Francisco Department of Public Health, similarly stated there is no centralized process for following up with people who missed second-dose appointments at a city-run vaccine clinic.

Though all the data from the different clinics will hopefully be properly entered into the California Immunization Registry — the state’s centralized system for tracking residents’ immunization records — Sanchez said there is “often a lag in our receipt of this data.”

In Santa Clara County, officials say they are “exploring additional approaches for reaching patients who miss their second-dose appointments.” Staff, in some instances and only at some of the vaccination sites, have called individuals who missed their second-dose appointments to follow up with them, but there are no set protocols in place.

Dr. Marty Fenstersheib, the county’s COVID-19 testing and vaccine officer, said he’s constantly reminding people of the importance of the second dose, even if the recommended three- to four-week time interval has passed.

“Some people think you can only get it if it’s within that window, but that’s not the case. You can go six weeks out and still have better protection than not,” he said.

Despite concerns raised about people skipping second doses, UCSF’s Rutherford said it should not be seen as a major issue in the nation’s vaccination campaign.

“If we get most people fully vaccinated, this is not a catastrophe that we have a small percentage of people who have only one shot,” he said. “My concern is just that we don’t want to see that number creep up even higher.”