States, cities face loss of vaccination programs and staff after ‘baffling' cuts to federal funding

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Millions of dollars have been pulled from state and local vaccination programs with no explanation, after a review of the funding agreements by the US Department of Health and Human Services.
Affected programs say they will probably have to cut staffers and services because of the shortfall, and they worry that vaccination rates will also drop as they lose the ability to assist people who are low-income or uninsured.
Immunization programs across the country are already struggling to address an increase in vaccine-preventable diseases. These include pertussis – also known as whooping cough – which has sickened more than 10,000 Americans and killed five children this year, as well as a smoldering outbreak of measles that has killed three people in the US and threatens to end the country's elimination status.
'That's the baffling part,' said one policy expert who spoke to CNN on the condition that they not be named for fear of government retaliation. 'Why anyone would create this disruption in the midst of the worst measles outbreak in 30 years.'
Most money spent by states on vaccination comes from the federal government.
The grant money, which is appropriated by Congress under Section 317 of the Public Health Services Act, enables states, territories and some large cities to collect data on vaccination, as well as provide shots to underserved children and adults. The funds also help monitor the safety of vaccines and fight misinformation. The money is doled out in five-year grants overseen by US Centers for Disease Control and Prevention, and the most recent awards were due to states on July 1.
This year, however, HHS conducted lengthy reviews of the awards, which delayed their arrival in some cases.
HHS Director of Communications Andrew Nixon said the reviews were part of agency cost-cutting efforts.
'The Defend the Spend initiative is a department-wide effort to ensure that taxpayer dollars are being used effectively, transparently, and in alignment with this administration,' Nixon said in a statement to CNN. 'As part of this oversight, grant recipients may be asked to provide additional information, which is essential to preventing waste, fraud, and abuse. HHS is committed to working all grantees to resolve outstanding issues as quickly as possible while maintaining the highest standards of accountability.'
Public health advocates say the latest funding cuts appear to be part of a larger pattern of efforts by HHS Secretary Robert F. Kennedy Jr. to disrupt and dismantle the America's vaccination infrastructure.
'Millions of children missed their routine vaccinations during the pandemic,' and never caught back up said Dr. Caitlin Rivers, director of the Center for Response Outbreak Innovation at the Johns Hopkins Bloomberg School of Public Health.
Vaccine hesitancy has also increased, driven by a deluge of misinformation, some of it now coming from official channels.
As a result, vaccination rates have dropped, and some communities are no longer protected by herd immunity, the threshold of vaccination required to prevent certain infectious diseases from easily spreading.
If state vaccination programs are not adequately resourced, 'we're just going to continue to fall further and further behind, and that sets the stage for things like measles and pertussis outbreaks, which we're seeing,' Rivers said.
Public health programs often become victims of their own success, she said.
'When there is a large public health emergency … there are huge investments made in public health, because we can see very clearly what the consequences are of having inadequate resourcing and inadequate infrastructure. But over time, those investments begin to work, and the threats recede, and we start to forget why it's so important to maintain those defenses,' Rivers said.
'And I think now, five years out of Covid, we're very clearly in the neglect cycle, and we're seeing a lot of the investments we made during the pandemic be pulled back,' she added.
Of 66 jurisdictions awarded federal immunization funding this year, about 40 received awards lower than their funding targets. And more than a dozen states and cities received lower awards this year than they did in 2019, just before the Covid-19 pandemic began, the last time these awards were offered through the CDC, according to a CNN analysis of federal data.
Massachusetts, New York, Indiana, California and Arizona were among those awarded less this year than in 2019, the year before the Covid-19 pandemic began.
'That's really, really unbelievable to us,' said one public health advocate who asked not to be named for fear of political retaliation for speaking out against the cuts. 'How could we come out of a pandemic with half of states being less prepared?'
Other states found that their awards were far lower than they'd been told to expect.
In January 2025, the CDC sent out a Notice of Funding Opportunity – essentially an invitation – to states, territories and certain large cities. It came with a funding target: the amount they could expect if their grant proposals were accepted.
Washington, for example, was told it could expect about $9.5 million, so the Department of Health planned for that amount for the 2026 fiscal year. When the state got its Notice of Award on July 1, however, it was for $7.8 million, an 18% reduction.
Massachusetts was told it could expect $7.7 million for the upcoming fiscal year, already a 20% reduction from its 2025 budget. When the award arrived, it was $1 million under the targeted amount, at $6.7 million, which means the department expects to operate with about 30% less funding next year than it has this year.
Colorado received almost $500,000 less than it expected, a decrease of about 5% from the amount it budgeted for, according to federal data
California, Illinois, Michigan and New York also received lower-than-expected funding awards, according to a CNN analysis of federal data.
Sometimes, the delays and errors in funding caused chaos: At least one state, Idaho, furloughed its immunization program staff with no notice after the money didn't arrive when expected. When the award did come through a day later, they were put back to work, but medical providers who reached out in the interim to submit their regular data updates had no one to help them and didn't know when services would be restored.
The cuts didn't just affect state health departments. The city of New Haven, Connecticut, had to lay off immunization positions that were supported by subawards it receives from the state grant. When the grant didn't arrive in time, the state directed the city not to incur any more expenses, and when the federal money did come through, it was 20% less than anticipated.
Chicago is also preparing to lay off immunization workers, according to multiple sources with knowledge of the city's plans, who asked not to be named because they feared retaliation by the Trump administration.
Not all awardees saw reductions, however. About two dozen jurisdictions, including Alabama, Idaho and Wyoming and Montana, got significant funding increases over their award targets for this year.
State officials who spoke to CNN for this story say they were given no explanation for why the awards were reduced or increased this cycle.
The cuts come on top of the loss of billions in unspent Covid relief funding that was being used by states, in part, to help staff immunization programs. In late March, HHS directed the CDC to roll back about $11.4 billion in Covid-era funding granted to state and local health departments. Another $1 billion was reclaimed from the Substance Abuse and Mental Health Services Administration.
A survey conducted by the Association of Immunization Managers found that the Covid money clawback alone has led to the elimination 579 staff positions in state vaccination programs.
After the new grant cuts, some jurisdictions said they would probably need to lay off even more workers but were trying to assess the changes that would be needed. Some programs said they hoped state funding could help fill the gaps.
In the past, the funding amounts that jurisdictions were told they could expect have been determined by a relatively simple formula that primarily relied on an area's population.
This year, however, federal officials deployed a more complicated formula that took into account population levels as well as how much of a state was rural and how many providers participate in the Vaccines for Children program compared with the overall population, according to a public health advocate familiar with the awards who asked not to be named for fear of political retaliation.
Immunization programs were told they could expect about $418 million in funding. All told, what they were awarded totaled roughly $398 million.
Changes to the funding formula don't appear to account for the reductions, however. The formula was applied to the target amounts that were distributed in January.
Instead, changes to the awards came after the HHS review, which in some cases delayed the release of the money and left programs hanging.
Hawaii, for example, received authorization to borrow up to $100,000 from the state government to pay salaries and cover operational expenses until its award came through, about two weeks late.
Public health advocates blasted the funding decision.
'Stripping 317 waiver funds combined with other losses is starving state and local public health budgets and is not just short-sighted, it's reckless,' said Dr. Brian Castrucci, president and chief executive officer of the nonprofit deBeaumont Foundation, which advocates for the public health workforce.
'We're watching the deliberate dismantling of the public health safety net in real time,' Castrucci said.