The computer contained the personal information of some 33,000 people who had applied to the Clear registered travel program, which is run by Verified Identity Pass Inc.
The laptop was reported stolen July 26 but turned up Tuesday morning in a cabinet in the same locked office at the airport from which it went missing, said Allison Beer, a spokeswoman for the company.
San Mateo County sheriff's Sgt. Wes Matsuura said today that investigators believe the laptop was stolen and returned, rather than simply misplaced. No one has been detained or arrested in connection with the case, but the investigation remains "highly" active, he said.
Beer said, "We do feel that we're a victim of a theft here and are looking for the investigation to figure out what happened."
The criminal investigation is being conducted by San Mateo County Sheriff's Office and San Francisco airport police, Matsuura said.
A preliminary investigation indicated that no information on the laptop was compromised, and the Transportation Security Administration is working to confirm there was no breach of information, Matsuura said.
"TSA headquarters in Washington, to my understanding, is determining whether any of the info was compromised or not," Matsuura said.
Information on the laptop includes names, addresses, birth dates and some applicants' driver's license numbers and passport information, but does not include applicants' credit card information or Social Security numbers, according to the company.
The TSA last week suspended Verified Identity Pass Inc. from enrolling new applicants after the reported theft of the unencrypted laptop.
The TSA also told officials at the San Francisco and other airports that use Clear to suspend enrollment, cease use of any unencrypted computers and secure devices until encryption can be installed.
Beer said today all computers had been encrypted as of late last week and Verified Identity Pass had completed an independent audit required by the TSA.
She said enrollment in the Clear program is expected to resume within the next couple of days.
Current customers have not been affected and will not experience disruption when using the Clear system, which allows travelers to get through security faster.
Verified Identity Pass operates at 17 airports nationwide and has signed up more than 200,000 travelers.