The federal government has denied New York City’s application for Head Start funding for the next five years, according to an internal memo Wednesday obtained by the Daily News.

In the email to city-contracted providers, the city’s Department of Education announced that after submitting a “strong, community-centered proposal,” it was not awarded grants this cycle for the federal program, which provides year-round child care to qualifying low-income families.

The top city official for early childhood education, Deputy Chancellor Simone Hawkins, testified during a City Council hearing in May that officials applied for about 4,000 federally funded Early Head Start and Head Start seats, down from nearly 5,900 in the last grant that expired over the summer. That number included nearly 900 more slots for infants and toddlers, while scaling back under-enrolled, preschool-aged programs.

It was not immediately clear what the rejection would mean in the long term for working families or the city’s broader financial picture. For now, Mayor Adams committed in April to covering any potential budget gaps with city tax levy.

“While this outcome is disappointing, we want to be clear: the city has committed significant local funding to ensure that E/HS [Early/Head Start] programs remain open and services continue for the upcoming school year,” Division of Early Childhood Education officials wrote.

A public schools spokesperson did not say how much city tax levy has been committed, but planned to brief the media on Thursday. A report by Comptroller Brad Lander found that, under the expired grant, close to one-third of Head Start providers received $71 million in federal funds through the city school system, in addition to other programs that get their funding directly from the federal government.

Going forward, officials told providers the city would “continue working closely with you to plan for next year, provide clear guidance, and ensure that your program has the information and resources needed to support families and staff.”

The uncertainty comes during a period of significant disruptions to the nation’s Head Start programs under the second Trump administration, including temporary funding freezes and threats of budget cuts, regional office closures, including in New York, and policy changes impacting undocumented children.

But New York City’s Head Start woes can actually be traced back to before the president took office, when it was entered into a federal program to boost enrollment. While the safety-net initiative expects a minimum of 97% seats filled to be considered fully enrolled, New York City Public Schools and its providers hovered around the mid-60s, according to education officials.

Not long after, a routine government audit in 2023 found issues in the city’s Head Start network with financial management, financial controls and child abuse and maltreatment, entering the system into a federal accountability program known as the “Designation Renewal System,” officials said.

The school system was then forced to reapply for the funding at the end of the last grant cycle, formally submitting its application in January.

How much New York City will have to foot the bill for Head Start will likely depend on what local providers receive from the federal government.

There are two ways local Head Start programs secure federal funding: either by working with the city’s school system and being awarded funds through that process, or contracting directly with the the Administration for Children and Families, a division of the U.S. Department of Health and Human Services.

While the federal government denied New York City’s application as a “super grantee,” it may still award funding to individual city-based providers. In that case, some or all of the grants could keep flowing to local programs, while cutting out the middleman.

The Administration for Children and Families did not immediately comment or provide a timeline for its next funding decisions.

“Everybody is waiting with bated breath,” one child care advocate said.