Texas officials have quietly restarted a controversial program to ask people on the voter rolls to prove their citizenship, sparking alarm that thousands of eligible voters could be wrongfully targeted.

The Texas secretary of state’s office has identified just under 12,000 people it suspects of being non-citizens since September, when the program restarted (there are more than 17 million registered voters in Texas). About 2,327 voter registrations have been cancelled so far. The vast majority of cancellations were because voters failed to respond to a notice giving them 30 days to prove their citizenship.

The secretary of state flags anyone as a suspected non-citizen if they register to vote and then subsequently visit the Texas department of public safety (DPS), the state’s driver’s license agency, and indicate they are not a citizen.

Local election officials in Texas’ 254 counties are then asked to review the names. If those officials cannot verify citizenship, they are required to send them a letter asking them to prove their citizenship within 30 days or else their voter registration gets cancelled.

But election officials in Harris county, the most populous in the state, are concerned about the accuracy of the data being used to challenge voters.

After the county mailed proof of citizenship requests to 2,796 people, 167 voters – nearly 6% of those contacted – responded with proof of citizenship. The state removed an additional 161 people from the list of people whose citizenship needed to be verified, according to a county official.

“We are not confident in the quality of the information we are being mandated to act upon,” Isabel Longoria, the county’s election administrator, said in an email.

In Fort Bend county, just outside of Houston, officials mailed notices to 515 people in October. About 20% responded with proof of citizenship and the rest were removed from the rolls, according to John Oldham, the county’s election administrator. Many of the people who responded said they had accidentally checked a box during their DPS transaction indicating they were not citizens, Oldham said.

In Cameron county, along the US-Mexico border, election officials have sent out 246 letter since September, almost all to people with Hispanic surnames, according to the Texas Monthly, which first reported the program restarted. About 60 people have been cancelled so far.

After the notices went out, a married couple who had heard about the notices came into the elections office to provide their naturalization papers, even though the couple’s citizenship wasn’t challenged, said Remi Garza, the county elections administrator.

“It saddened me too,” Garza said. “People who shouldn’t have to be concerned about this type of proving citizenship felt that they had to do that.”

Voting rights groups say they are trying to better understand the process the state is using, but are concerned eligible voters are getting targeted.

“​​A US citizen voter who gets a challenge letter is understandably intimidated. And especially for naturalized US citizens, who went through an entire bureaucratic process to be able to vote, getting a letter that accuses them of being an ineligible voter is particularly intimidating,” said Nina Perales, an attorney with the Mexican American Legal Defense and Educational Fund. “People will naturally assume, based on this official correspondence, that they might have made some kind of mistake, or that they are not proper voters.”

The program had been on hold since 2019, when a federal judge ordered Texas to stop a similar, error-filled, effort that he described as “ham-handed”. As part of a settlement in that case, Texas agreed to only flag people if they registered to vote prior to the DPS visit in which they indicated they weren’t a citizen. It also agreed to reinstate and challenge voters who provided proof of citizenship, even if it was outside the 30-day window.

The citizenship check comes as Republicans have moved to blunt the rapidly growing political power of Texas’ non-white population. Texas prosecutors have sought criminal punishments for people, including non-citizens, who make voting mistakes and the attorney general, Ken Paxton, has zealously pursued claims of voter fraud, which is exceedingly rare in Texas and elsewhere.

Bruce Elfant, whose office oversees voter registration in Travis county, said his office so far has internally been able to confirm that less than 100 of the 300 to 400 people flagged by the secretary of state’s office were citizens. Most in the group had been flagged because of clerical errors, he said. His office has not yet sent out any challenge notices and is waiting for more information before it does so.

In El Paso county, state officials referred 4,000 suspected non-citizens for review, and around 300 had already offered proof of citizenship, said Lisa Wise, the county’s election administrator. The county isn’t currently cancelling the registration of any voter who doesn’t respond, she said.

Federal law prohibits officials from conducting mass voter cancellations within 90 days of a primary election. Texas’ primary is on 1 March, so the state can’t remove anyone who doesn’t respond to a proof of citizenship letter until later this spring.

Thomas Buser-Clancy, a senior staff attorney with the Texas chapter of the American Civil Liberties Union, said his organization was trying to understand why eligible voters were being flagged, but it was clear “something is not going right”.

“Even if your system flags one eligible voter and threatens to remove them, that’s a problem,” he said. “If you have hundreds, and if you add it up across counties, you’re probably getting to thousands of eligible voters, being threatened with removal.”

Sam Taylor, a spokesman for the Texas secretary of state’s office said he was confident in the data.

“We’re following the settlement agreement exactly as we’re supposed to. If the counties have additional information where they’re able to cross people off the list who have in fact become citizens and they’re lawfully registered to vote, that’s great. That’s how the process is supposed to work.”

But Buser-Clancy noted that those who were able to affirm their citizenship likely only represented a fraction of the eligible voters who were probably affected.

“Those people are the lucky ones that both received the notice, like actually went through their mail, looked it up, and had the documentation on hand to send in,” he added. “What that tells you is that there’s some other percentage of people who are going to be removed from the rolls even though they’re eligible voters.”