Parents of children under 5 will have to wait until at least April to get their kids vaccinated against Covid-19, after the Food and Drug Administration and Pfizer this week abruptly delayed plans to get the shots authorized on a fast-track basis.

The FDA had originally planned to authorize the first two doses of what will ultimately be a three-dose vaccine as soon as this month. However, Dr. Peter Marks, head of the FDA’s vaccine division, said updated data submitted by Pfizer and BioNTech did not support the plan to get the first two doses out early. Marks acknowledged that the decision was abrupt, but said the FDA was following the science.

“The data that we saw made us realize that we needed to see data from a third dose in the ongoing trial in order to make a determination that we could proceed with doing an authorization,” Marks told reporters during a call Friday, without providing specifics on the data. 

Acting FDA Commissioner Janet Woodcock said the drug regulator had sought to act swiftly  to protect children against omicron as Covid hospitalizations among the youngest rose to record levels in recent weeks. However, the FDA’s safety and efficacy standards required the agency to wait for more information on the third dose, Woodcock said. 

“The goal was to understand if two doses would provide sufficient protection to move forward with authorizing the use of the vaccine in this age group,” Woodcock said in a statement. “Our approach has always been to conduct a regulatory review that’s responsive to the urgent public health needs created by the pandemic, while adhering to our rigorous standards for safety and effectiveness,” she said.

“Being able to begin evaluating initial data has been useful in our review of these vaccines, but at this time, we believe additional information regarding the ongoing evaluation of a third dose should be considered,” Woodcock said.

Dr. Paul Offit, a member of the FDA’s vaccine advisory committee, said the fast-track plan was based on the assumption that the third dose was safe and effective, but there’s no guarantee that will be the case once the final data is submitted.

“Imagine us approving it after two doses and then finding out later that the third dose was unsafe and then having to pull back,” said Offit, a pediatrician and director of the Vaccine Education Center at Children’s Hospital of Philadelphia. “I’m glad that we’re going to wait until we have all of the data to make that decision.”

The FDA had come under pressure in recent weeks from some parents and physicians to quickly expand eligibility to protect toddlers through 4-year-olds as the omicron variant swept the country. Children under 5-years-old are the only age group left in the U.S. that is not eligible for vaccination. 

Nearly 5,200 children were hospitalized with Covid on Jan. 18, according to a seven-day average of data from the Department of Health and Human Services, twice as many as the prior peak during the fall of 2021. That figure has since fallen to about 3,000 as of Friday, HHS data shows. 

The American Academy of Pediatrics, in a statement Friday, said although the news was frustrating to many parents, it’s important to have a rigorous review process to ensure a safe and effective vaccine.

“A careful, robust and transparent process to evaluate the evidence for the vaccine in this age group is essential in order for parents to have confidence in offering the vaccine to their children,” the AAP said.

The problem is that two doses of Pfizer and BioNTech’s vaccine did not produce an adequate immune response in children aged 2 through 4 during clinical trials. The companies are evaluating a lower, 3-microgram dose level in kids under 5, compared to older children and adults who get 30-microgram shots.

Pfizer and BioNTech amended their clinical trial in December to study a third dose to determine whether that would produce the immune response needed to protect against Covid. The companies had said all along that data would not be ready until April.

However, the rapid rise of omicron over the holidays and through January created what Pfizer called an “urgent public health need” to get kids in this age group vaccinated. Marks said the FDA’s sudden decision to delay authorization should not impact parents’ confidence in the vaccine. He said the shift shows that the FDA takes its responsibility seriously and makes decisions based on the data as it emerges.

“I hope this reassures people that the process has a standard, that the process is one that we follow,” Marks said. “And we follow the science in making sure that anything that we authorize has the safety and efficacy that people have come to expect from our regulatory review of medical products.”

Wayne Koff, CEO of the Human Vaccines Project and a professor of epidemiology at Harvard, said there’s good reason to expect the third dose will improve the effectiveness of the vaccine in children under 5-years-old. Booster doses have proven effective at preventing severe illness in other age groups, Koff said, and the vaccine should really be considered a three-dose regimen in general across age groups at this point.

Offit said the Covid shot will likely become a routine childhood vaccine in the future, like immunization against polio. The U.S. eliminated polio in the 1970s, but it still vaccinates kids because the virus continues to circulate in some corners of the world. Public health experts largely agree that the eradication of Covid is unlikely at this point.

“The fact remains, we’re going to need to have a highly protected population for years and decades. I suspect this will become a routine childhood vaccination,” Offit said.

Though some parents may feel that it has taken too long to expand access to the vaccine, Koff said the FDA has accelerated the process as much as possible by progressively lowering the eligibility age while adhering to safety and efficacy standards.

“In the beginning you have to show the vaccine is safe and effective in the adult population,” Koff said. “Once you have shown that, then you’re able to go down in terms of the age of the adolescents and then eventually the younger kids and then eventually the infants.”

Offit said children under the age of 18 get infected less frequently and less severely, which is why vaccination has focused on the older populations first. As parents wait for the vaccine, they should build a “moat” around their kids who aren’t eligible by making sure everyone who is in contact with them has gotten their shots, he said. 

While about 75% of U.S. adults are fully vaccinated with two doses of the Pfizer or Moderna shots or one dose of the Johnson & Johnson vaccine as of Thursday, that figure is lower for kids. Roughly 57% of those aged 12 to 17 are fully vaccinated, according to the CDC, and 24% of those 5 to 11.

— CNBC’s Nate Rattner contributed to this report.