(CNN) — The US Department of Health and Human Services on Wednesday unveiled a pilot program for the National Institutes of Health to tap into Medicare and Medicaid data in its search for the root causes of autism.

The database — which HHS said will draw from insurance claims, medical records and data from wearable technology such as smartwatches — is one of the first steps in HHS Secretary Robert F. Kennedy Jr.’s bid to find the causes of autism “by September.”

Early signals from health officials that they would build a database to track autism were met with swift rebuke from advocacy organizations and doctors.

NIH Director Dr. Jay Bhattacharya’s initial description last month of a “new autism registry” with “broad coverage” of the US population raised red flags and questions about privacy, the Autism Science Foundation said in a statement shortly after the news. The Autism Self Advocacy Network lambasted the project as an example of how the administration has “completely frozen out autistic people.”

HHS nodded to those concerns in its announcement Wednesday. It said the NIH and the Centers for Medicare & Medicaid Services will start with a data use agreement focused on Medicare and Medicaid enrollees diagnosed with autism spectrum disorder and then establish a “secure tech-enabled mechanism” that will share data with “timely, privacy and security compliant data exchange.” The agencies will eventually build out the pilot database to share data on chronic illnesses and their economic burden, HHS said.

“Ever since the registry was first announced, there was an enormous sense of fear in the autism community, and they have concerns: Who’s going to have access to data? How are those data going to be used?” Helen Tager-Flusberg, director of Boston University’s Center for Autism Research and leader of the Coalition of Autism Scientists, told CNN.

There are also limitations to CMS data, Tager-Flusberg said. “If you’re talking about Medicare and Medicaid, that only focuses on certain portions of the population.”

Medicaid is a federal and state partnership covering low-income adults and children. Medicare is a federal program primarily for Americans 65 and older, although younger people with disabilities are also enrolled.

There are permissible uses of CMS data for medical research but very stringent privacy laws, Jeff Wurzburg, former HHS general counsel and a health care regulatory attorney at Norton Rose Fulbright, said before Wednesday’s announcement. “One of the primary, overarching goals of CMS is protection of the beneficiary. So it’s certainly legitimate and reasonable to raise questions about how this data will be collected and protected.”

An HHS spokesperson said Wednesday, “Data with personal identifiers are subject to federal privacy laws and regulations. This data platform would be fully compliant with these laws and regulations to protect Americans’ sensitive health information.”

Autism advocates and scientists have also questioned Kennedy’s claim that health agencies would find the causes of autism by September, a timeline that Bhattacharya has already appeared to walk back.

“Science happens at its own pace. We’re accelerating and cutting the red tape that normally comes with putting together a scientific program like this,” Bhattacharya said April 22. “We’ll have, I hope, in September, something that in place where the scientists that want to want to compete for these [grant] awards will be able to do that.”

‘Flood’ of concerned calls about registry

The lack of clarity around how this autism data would be used, who would have access to it and patients’ consent to its use has spread fear throughout the community.

The Autism Science Foundation was “flooded” with calls, emails and texts after Bhattacharya’s initial comments about a registry, co-founder and President Alison Singer said. The latest announcement did not abate those concerns.

“The one that concerns me the most is people with autism who are saying that they’re afraid to go to the doctor; families who have said they have concerns about their toddlers, but they’re afraid to take them for diagnosis,” Singer said. “It’s having a chilling effect on medical care.”

Singer said the foundation is supportive of registries, which can be valuable for tracking care and outcomes over time. But the lack of details about privacy – or dialogue with the autism community before launching the project – has made it difficult to quell those concerns.

“We’ve tried to allay the fear around a registry in general, but we can’t really do that until there’s more information shared from the administration about how it’s going to be put together.”

The HHS spokesperson said, “Let’s be clear: this initiative is about advancing science, improving care, and supporting families. Understanding the scope and burden of a condition is standard in public health and crucial to driving funding, improving services, and informing policy.”

Other autism advocates are adamantly opposed to the idea of a registry, citing the way Kennedy has spoken about people with autism. The HHS secretary recently said autism is part of a “chronic disease epidemic” that “destroys” children and families, and he faced criticism for saying people with autism will “never” pay taxes, hold a job, play baseball, write a poem, go on a date or use a toilet without assistance. Kennedy later said he was speaking about people with “severe” autism.

“This is setting a precedent that it is somehow OK to weaponize somebody’s medical diagnosis for political reasons,” said Nicole Clark, a nurse and co-founder of the Florida-based Adult and Pediatric Institute for Health and Wellness.

“Someone having a medical diagnosis going into a registry to prove financial burden — what’s the end goal of this? What are we looking to do here?” asked Clark, who also has two young children with autism.

She described conversations with other health care providers about the fear already circulating among autistic people and their families, with some patients asking their doctors whether they can get their autism diagnosis removed from medical records.

“Are we going to use this data to create fear within providers to not want to diagnose?” Clark asked. “This just feeding off of the fear of what we don’t understand.”

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