The Transportation Department said it will use a presidential memo calling for punishing “anarchist jurisdictions” when deciding which cities should get money under a coronavirus grant program.

The American Public Transportation Association said the declaration could undermine applicants for the pandemic safety grants from Seattle, Portland, Ore., or New York City, the first three jurisdictions the Trump administration has deemed to be “permitting anarchy.”

President Trump has criticized elected officials in those cities for their handling of protests in response to the killing of George Floyd in police custody, racial injustice and Trump administration policies.

The move also comes as critics have slammed the Trump administration — and the Transportation Department under Secretary Elaine Chao — for not executing policies needed to subdue the coronavirus. The pandemic has caused more than 217,000 deaths.

According to polls, Trump is trailing in his reelection bid, and he sees a political upside in sparring with the leaders of liberal strongholds.

Pointing to hundreds of billions of dollars the federal government sends to states and localities, Trump said in the memo last month that he would “not allow Federal tax dollars to fund cities that allow themselves to deteriorate into lawless zones.”

The $10 million in coronavirus transit grants are meant to spur innovative “exposure mitigation measures,” such as real-time notifications so rail and bus passengers can avoid crowded commutes, according to a regulatory filing. The grants also target research in contactless payment systems and improved disinfection techniques.

But along with the usual boilerplate language in the Oct. 8 Federal Register notice outlining requirements for the competitive grant program was a sentence some city officials said was both novel and disturbing.

“In addition, the Department will review and consider applications for funding pursuant to this Notice in accordance with the President’s September 2, 2020 memorandum, entitled Memorandum on Reviewing Funding to State and Local Government Recipients of Federal Funds that Are Permitting Anarchy, Violence, and Destruction in American Cities, consistent with guidance from the Office of Management and Budget and the Attorney General and with all applicable laws,” the notice read.

The National Association of City Transportation Officials said Wednesday that the administration is seeking to use “arbitrary and politically-motivated pretext to deny cities and transit agencies” safety funding. The grant language sets a “dangerous precedent that could undermine future economic recovery efforts. Denying transit agencies funding obstructs their ability to develop best practices to make transit safer for millions of riders and workers.”

David Bragdon, of the advocacy group TransitCenter, said Chao’s “willingness to expose innocent transit riders and essential transit workers to greater risk of covid-19 just because of Donald Trump’s unrelated personal vendetta against certain local elected officials is both reckless and un-American.”

In a statement, the Transportation Department said: “Presidential directives are not discretionary, consistent with all applicable statutory requirements.”

The statement noted that the department had, earlier this year, awarded $25 billion in funding to transit agencies “in a record 6 days,” as part of far-reaching coronavirus-relief legislation. It also pointed to the department’s distribution of more than 100 million face coverings.

The new notice on the transit research funding also “was issued quickly so that these funds can be distributed as soon as possible to transit agencies during this public health emergency,” according to the statement. The deadline to apply is Nov. 2.

Last week, union leaders called the Transportation Department’s decision to reject their petition calling for an emergency federal mask mandate on planes, trains and buses “tone deaf and stubborn.” The department said, in denying the petition, that it “embraces the notion that there should be no more regulations than necessary.”

The ultimate effect of the Transportation Department’s reliance on Trump’s “anarchy” memo remains uncertain.

Representatives from Seattle and Portland said the cities are exploring their legal options. It is unclear, for example, whether the regional transit agencies covering those cities might be able to apply on their own, bypassing the “anarchist jurisdiction” label put on the cities themselves.

Laura Feyer, a spokeswoman for New York Mayor Bill de Blasio (D), noted that the state runs the subway and bus system in the city. The Metropolitan Transportation Authority, in turn, said any possible application for the coronavirus transit grant remains “under review.”

Feyer said no other federal departments have cited Trump’s “anarchy” memo in grants being sought by New York City. But if such interference materializes, or federal officials take steps to withhold resources more broadly, the city is prepared, she said.

“This is nothing more than political retribution. If the Trump administration tries to take away our funds, we’ll see them in court,” Feyer said.