The Trump administration has long taken aim at the state and, more specifically, New York City for “sanctuary city” policies that limit cooperation with ICE. But Mr. Wolf’s decision to suspend enrollment for the programs turned what had most recently been a public relations campaign against local politicians into a punitive policy affecting possibly millions of New Yorkers.

“This is obviously political retaliation by the federal government, and we’re going to review our legal options,” Rich Azzopardi, a senior adviser to Gov. Andrew M. Cuomo, said late Wednesday night.

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New Yorkers will not be able to enroll in “Trusted Traveler Programs,” which allow people to cut through long lines at airports if they pass a pre-clearance with the Department of Homeland Security. Participants are granted expedited processing after international travel through the Global Entry program; from Canada through the NEXUS program; and from Canada and Mexico through the SENTRI program.

The Green Light Law was passed last year by New York’s Democratic Legislature and was signed by Mr. Cuomo, a third-term Democrat and frequent antagonist of President Trump. Under the new law, county and state motor vehicles departments could accept applications for licenses, regardless of immigration status.

It provoked a sharp backlash in some moderate suburban communities as well as in some more conservative areas upstate. Several county officials refused to comply or sued to stop the law, though it proved popular in liberal enclaves like New York City.