Illinois doctors were ecstatic in July when Gov. JB Pritzker made it easier for some low-income children to get vaccinated.

Pritzker reversed a state rule that required physicians to pay up front for expensive vaccines for their patients who are part of the state-run Children’s Health Insurance Program, known as CHIP. Doctors had sounded the alarm for years that shouldering that financial burden forced them to turn away patients on CHIP, leaving those kids potentially unvaccinated.

Even the Chicago Department of Public Health stopped vaccinating kids on CHIP who didn’t live in the city because of the cost. (The city resumed the immunizations after Pritzker’s policy reversal.)

But now that CHIP vaccinations are free to doctors again, the state is running out of them. On the cusp of flu season, doctors are worried about flu shots in particular.

“I have no flu vaccine for CHIP,” said Dr. Jihad Shoshara, president of west suburban Pediatric Health Associates, a large provider in DuPage County for low-income children. “Flu season is coming and we have a subset of our pediatric population that we can’t vaccinate.”

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He’s telling parents to hold on. The practice’s sickest patients will get flu shots first; that includes children with chronic conditions like asthma and diabetes.

The Illinois Department of Public Health didn’t expect such a surge in demand from physicians who are ordering vaccines for their patients on CHIP. Pritzker made shots free to physicians on July 1.

What’s more, in February, when it was time to pre-order flu vaccines, the state didn’t include shots for kids covered by CHIP. That was before Pritzker’s policy change. Physicians who did immunize patients on CHIP before the policy change bought vaccines on their own and waited for insurers to reimburse them, if they did at all.

In an effort to calm physicians nervous about shortages this fall, the Illinois Department of Public Health issued a memo on Oct. 11.

“We are listening and are here to assist and resolve as best as we can,” wrote Gina Lathan, chief of the immunization section of the Department of Public Health.

The state would prioritize doses for doctors based on immediate need, she wrote, and limit the amount of vaccines physicians could receive as Illinois waited for more immunizations from manufacturers.

The memo said Illinois requested a second bulk order from vaccine manufacturers, and that’s expected to arrive around Oct. 25.

In a follow-up Oct. 22 memo, public health officials addressed concerns about flu shots specifically. They told doctors they could use vaccines reserved for their patients with private insurance for their CHIP patients. Before, that wasn’t allowed. Doctors could expect flu shots to arrive within two weeks.

Jennie Pinkwater, executive director of the American Academy of Pediatrics’ Illinois chapter, said the state was “kind of a victim of your own success.”

Doctors wanted to make sure they had enough vaccines in stock to treat their patients on CHIP who skipped or delayed vaccinations when they had few places to get immunized. This was when doctors were turning away patients on CHIP, before Pritzker reversed the policy.

The Democratic Pritzker administration this year hustled to change the state policy they inherited from former Republican Gov. Bruce Rauner. There was a nationwide measles outbreak, and over the summer, families with children on CHIP needed to find doctors to give them shots required for school.

Illinois has already spent $13 million of the $18 million it budgeted for CHIP vaccines, and the fiscal year just began in July. A spokesman for the state Department of Healthcare and Family Services, which oversees the CHIP program, said the state would increase the budget if needed.

Kristen Schorsch covers Cook County politics for WBEZ. Follow her @kschorsch.