The programs, like Global Entry, are meant to help travelers move through customs lines faster. But New Yorkers are no longer allowed to sign up or renew their memberships.
Federal officials said in a letter the suspension comes in response to a new state law that recently took effect.
Travelers at John F. Kennedy Airport told CBS2's Reena Roy on Thursday they were shocked to hear about the new federal order.
"I think for all New Yorkers it's inconvenient," resident Raj Singh said.
"Now it means whenever I want to travel, coming back here there are gonna be long lines after travel. My flight is like 17 hours," another traveler said. "The problem is the Trump administration has been anti-immigrant."
Acting Secretary Chad Wolf initially dropped the bombshell on Wednesday night on Fox News.
"We sent a letter to New York indicating, because they took these measures, that New York residents are no longer eligible to enroll in these Trusted Traveler programs," he said.
Wolf referred to New York State's sanctuary "Green Light law," which allows undocumented immigrants to apply for drivers' licenses without providing a Social Security number -- instead, using passports and IDs from other countries.
Massive lines formed at DMV's across the state after the law went into effect in mid-December.
Wolf called the law disappointing, saying it's a major security threat because it prohibits access to DMV data that's needed by U.S. Immigration and Customs Enforcement (ICE) as the agency builds cases and investigates criminal networks. He added that data is also used for trade and travel, necessary for background checks when someone applies for a Trusted Traveler program.
"We no longer have access to make sure that they meet those program requirements," he said.
All Global Entry applicants undergo rigorous background checks and in-person interviews before approval.
UPDATED STATE, FEDERAL INTERNATIONAL TRAVEL INFORMATION
The program, and several similar ones, allow expedited clearance for pre-approved, so-called low risk, travelers. Meaning, faster security and customs lines for members.
Some travelers told CBS2 the longer wait times without one of those fast passes will be worth it in the end.
"Sometimes you have to slow things down to get things right," said Heather Giambalvo of Suffolk County.
"We need to protect country. Absolutely, that's first priority," Len Giambalvo added. "I'd rather take a little inconvenience to make sure things are safe."
"A criminal alien, freed by the sanctuary city of New York, was charged with the brutal rape and murder of a 92-year-old woman," he said. "The killer had been previously arrested for assault. But under New York's sanctuary policies, he was set free. If the city had honored ICE's detainer request, his victim would still be alive today."
Speaking on public radio on Thursday, Gov. Andrew Cuomo said he was blindsided by the New York lockout, calling it a political stunt, and adding the Trusted Traveler programs have nothing to do with New York's Department of Motor Vehicles database, CBS2's Hazel Sanchez reported.
"You have to go to a federal office or sit with a federal official, do an in-person interview, provide them data and then you get signed up. So they don't need anything from me because they have you right in front of them. So, it's all politics," Cuomo said.
The DHS said more than 175,000 New Yorkers will be kicked out of Global Entry by the end of 2020.
"They are unfairly paying the price for it because our governor and Democrats in New York are passing dangerous legislation that is putting illegal immigrants before citizens," Republican Assemblywoman Nicole Malliotakis said.
The agency added TSA precheck is not on the list of affected programs, but it could be in the future.
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