The number of babies born in Puerto Rico with microcephaly and other birth defects caused by the Zika virus appears to be unexpectedly low — so low that experts are beginning to question whether the actual count is being significantly underreported by authorities on the island.

As Zika surged across the Americas last year, US health authorities warned that Puerto Rico was facing a perfect storm — and braced for a large number of pregnancies affected by the virus.

But, to date, Puerto Rico has reported only 16 cases of congenital defects associated with Zika, even though more than 3,300 pregnant women are known to have contracted the virus and several times that number are believed to have been infected.

By contrast, US states and the District of Columbia, where the threat posed by Zika was thought to be much lower overall, have registered congenital defects in 63 fetuses or newborns among 1,300 pregnant women who have contracted the Zika virus.

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Some observers believe Puerto Rico, which is heavily dependent on tourism, is downplaying the scale of its Zika problem.

“Puerto Rico’s not escaping this. They’re just hiding,” one former US official said of the situation. The individual, who spoke on condition of anonymity, said months ago it was clear “dozens and dozens” of babies in Puerto Rico bore the hallmarks of Zika damage. But territorial health officials declined to label most of them cases of Zika congenital syndrome.

“They’re kind of in denial about what the problem is,” the former official said. “And six months, a year, two years from now there will be all these babies who aren’t learning and all these problems that will come to light.”

Puerto Rico’s health department did not respond to a request for comment, nor did its top epidemiologist.

Last October, without fanfare, the Centers for Disease Control and Prevention stopped reporting the outcomes of pregnancies in US territories in which women had been infected with Zika. Without providing details, the agency simply said that Puerto Rico wasn’t counting cases the same way.

“CDC is using a consistent case inclusion criteria to monitor brain abnormalities and other adverse pregnancy outcomes potentially related to Zika virus infection during pregnancy in the US states and territories. Puerto Rico is not using the same inclusion criteria,” the CDC website states.

Dr. Margaret Honein, chief of the CDC’s birth defect branch and a senior member of the agency’s Zika response team, said an agreement between the agency and other jurisdictions that contribute to its Zika pregnancy registries prevented her from providing specific details about how Puerto Rico’s case definition varies from the CDC’s without the explicit permission of authorities there.

“We have an ongoing collaboration with Puerto Rico department of health,” she said. “And we have ongoing discussions about working to align our case definitions. But at this time we’re not fully aligned.”

Last August researchers from the Puerto Rico health department and the CDC published a study predicting that Zika’s first wave of activity would strike a large number of pregnancies there, based on analyses factoring in the percentage of the population thought to be infected and the number of pregnant women on the island.

The study, published in the journal JAMA Pediatrics, projected that between 100 and 270 babies with Zika-induced microcephaly would be born between mid-2016 and the same time in 2017.

That study didn’t forecast figures for a host of other birth defects that Zika is known to cause but that are not always readily apparent shortly after birth, including destruction of brain tissue, damage to newborns’ optical nerves, and partial or total hearing loss.

A more recent study from the CDC mined the US Zika pregnancy registry to try to get a clearer picture of how often infections in pregnancy lead to birth defects in infants.

According to that study, 5 percent of babies born to women with confirmed or suspected Zika infection during pregnancy had Zika-related birth defects; when the researchers only included women with confirmed Zika infection, the rate was 10 percent.

And when confirmed infection occurred in the first trimester of pregnancy — when the risk Zika poses to a developing fetal brain is highest — 15 percent babies born or fetuses lost had Zika-related defects.

Read more: Obama administration declares Zika public health emergency in Puerto Rico

It’s not possible to perform the same calculations for Puerto Rico. The health department’s weekly report does not indicate how many of the 3,356 pregnancies with confirmed Zika infections have been completed.

Questions about Puerto Rico’s Zika birth defects count have started to appear in local newspapers. A former health secretary, Dr. Johnny Rullán, described the situation as Puerto Rico’s “Zika baby puzzle” in a recent column in the San Juan newspaper, Nuevo Dia.

When Zika first hit Puerto Rico, Rullán was brought in to advise the government on how to handle the new threat. He quit after the territorial government, under pressure from residents, rejected a plan to conduct aerial spraying to tamp down populations of the mosquitos that transmit Zika.

In the column, Rullán suggested there was evidence pointing toward substantially more births affected by Zika than have been reported. He urged the health department to follow up on babies born to women who may have been infected with Zika, because it needs to plan to deliver services to the affected children.

“If we do not identify them early, we can not give them the benefit of early interventions to avoid the ton of rehabilitation,” he wrote.

When contacted by STAT, Rullán declined to comment further, saying it was up to the Puerto Rican health department to respond to the questions he raised.

“I recommend you get the PR health officials to react to it!” Rullán said. “You have to ask them!”

Dr. Jose Cordero, a professor of public health at the University of Georgia who has been tracking Zika-related birth defects as part of an international study, offered a possible explanation for why Puerto Rico is reporting such a low number of affected pregnancies.

Cordero said the CDC has been casting a broad net for possible signs of damage by the virus, including in the offspring of all women infected during pregnancy if there’s any sign of the types of birth defects associated with Zika.

That doesn’t appear to be the way health authorities in Puerto Rico are counting cases, he said.

Cordero said he was recently invited to a Zika issues planning meeting on the island. There he heard Dr. Miguel Valencia, director of the health department’s division for infants with special medical needs, describe the case definition Puerto Rico is using to identify Zika birth defect cases.

“As I understand the conversations that I had with Dr. Valencia he was going in the opposite direction [of the CDC] — that the child must have microcephaly before he’s considered to be affected,” Cordero said.

Cordero called Valencia “the keeper of all those numbers. And he’s certainly keeping them very close to his vest.”

Valencia did not respond to a request for comment.

Does Cordero believe Puerto Rico’s official report on Zika-affected infants represents the true number in Puerto Rico? “I don’t know. I don’t know the answer to that,” he said. “I think that one has to be intrigued in terms of the differences.”

Cordero said part of the problem may relate to the number of challenges Puerto Rico is facing. The island’s finances are in dire straits, making Zika only one of several major issues the territorial government must address.

The economic situation has also led to the migration of Puerto Ricans elsewhere. Some women who know they’re going to give birth to a baby with Zika birth defects or who have done so in Puerto Rico may move to the US mainland in the hope of accessing better services for the child, Cordero said. That could also contribute to a lower-the-expected count of affected pregnancies on the island.

“There are many variables here,” Cordero said.