The Trump administration is threatening to withhold federal funds if the Chicago Transit Authority doesn’t increase the presence of law enforcement in the wake of a recent attack in which a woman was set on fire while riding a train.

In letters addressed to Mayor Brandon Johnson and Gov. JB Pritzker, the Federal Transit Administration blames the city and state or the attack on Bethany MaGee last month.

“Creating a safe, reliable transit system is the responsibility of leaders at every level,” FTA Administrator Marc Molinaro says in a letter sent late Monday to Johnson. “CTA, the city of Chicago and the state of Illinois have failed to meet this obligation. If CTA does not promptly increase its law enforcement presence, FTA will act, including by withholding federal funds.”

It’s the latest dispute between the White House and the Johnson and Pritzker, including an attempt to deploy the National Guard to Chicago to deal with crime and the Department of Transportation’s threat to withhold $2 billion in funding for the extension of the CTA’s Red Line because of minority-contracting provisions.

"I don’t need a letter from the Trump administration to tell me what my priorities are," Johnson said Tuesday morning.

"As I’ve said repeatedly, we do have to look at what the security apparatus looks like for public transportation. (The Chicago Police Department) plays a role in that. The Department of Public Health plays a role in that. All of us play a role in ensuring that CTA riders experience maximum safety," he said.

The mayor has traditionally controlled the CTA through the appointment of board members and nomination of the authority’s president, although that’s set to change. Currently, the mayor has four appointees to the seven-member board, and the governor has three.

Pritzker, who has been frequent and forceful critic of Trump, again took aim at the White House while pointing to public-safety improvements that were part of the transit overhhaul and rescue plan passed by the state Legislature in October.

“Instead of focusing on serious, coordinated solutions, the Trump administration is politicizing a heinous tragedy and doing nothing that makes our communities safer," Pritzker said in a written statement. "This year, Illinois passed public transit reform that includes increased funding for public-safety programs, including establishing a dedicated task force to coordinate deployments across law enforcement agencies to combat violent crime on public transit.

"If the Trump administration was truly committed to reducing crime, they would release funding for crime prevention and law enforcement and support Illinois with more FBI, ATF, and DEA personnel. Instead, they are threatening to withhold federal funding for transportation that actually makes people’s lives safer. Illinois remains focused on real, sustained strategies that improves public safety for riders, workers and families.”

At a press conference Tuesday morning, Pritzker said, "Threatening state and local government to take away federal funds for a purpose they’re not allowed to."

Molinaro said in his letter that the attack on MaGee, which made headlines nationwide, was evidence of broader problems at the CTA.

"Given high crime rates on CTA property, this incident is not isolated and reflects systemic failures in both leadership and accountability at all levels and cannot be tolerated,” his letter says. "The attack on Ms. MaGee was preventable. Transit leaders and elected officials who fail to enforce basic laws and permit disorder to erode the integrity of their systems are making deliberate choices that endanger riders.

Molinaro said the CTA failed to update its Public Transportation Agency Safety Plan and “maintain a safe operating environment for workers and passengers, including failing to implement adequate mitigations to address a years-long pattern of elevated assaults on workers and riders, and serious violent crime.”

He said the CTA must update its safety plan by the end of December and “develop a verifiable security-enhancement plan” that must be submitted to the Federal Transit Authority for approval.

"The CTA is in receipt of a Special Directive from the Federal Transit Administration. We have reviewed the document and will respond within the requested timeline," the CTA said in a written statement.

NBC-5 was first to report the funding threat.

— Justin Laurence contributed.