That has happened to Abdulla Darrat, an urban planner from Queens who said he was flagged for extra scrutiny all eight times he flew since June. When he tries to check in online, a message tells him to check in at the airport, where he receives a boarding pass marked with “SSSS” indicating that he must undergo enhanced screening. His name has been handwritten on a card at the podium where an agent checks passengers’ identification, he said.

“They pat me down,” Mr. Darrat, 31, said. “Then they pull out every single article of clothing in my bag. They take out every shirt and every pair of pants.”

After the checkpoint search, which includes swabbing his luggage to check for explosive residue, he said he was often stopped at the gate before being allowed to fly. He said he assumed that the extra scrutiny was because he had flown to Libya to visit relatives. He also expressed support for protests against Muammar el-Qaddafi in 2011, but the extra scrutiny did not happen until this summer.

“It adds this whole air of suspicion about me to everybody on the plane,” he said.

Critics argue that the problem with what the agency calls an “intelligence-driven, risk-based analysis” of passenger data is that secret computer rules, not humans, make these determinations. Civil liberties groups have questioned whether the agency has the legal authority to make these assessments, which the T.S.A. has claimed in Federal Register notices and privacy disclosures about the initiative. Privacy advocates have also disputed whether computer algorithms can accurately predict terrorist intent.

The airline industry has supported the expansion of PreCheck and using data about travelers to decide who should receive more or less scrutiny at checkpoints, to reduce security bottlenecks and focus resources on higher-risk passengers.

At the heart of the expanded effort is a database called the Automated Targeting System, which is maintained by the Department of Homeland Security and screens travelers entering the United States.

Data in the Automated Targeting System is used to decide who is placed on the no-fly list — thousands of people the United States government has banned from flying — and the selectee list, an unknown number of travelers who are required to undergo more in-depth screening, like Mr. Darrat. The T.S.A. also maintains a PreCheck disqualification list, tracking people accused of violating security regulations, including disputes with checkpoint or airline staff members.