Mr. Greenspan defended the deal by saying his company was forcing law enforcement agencies to be transparent, unlike other DNA testing companies.

“Law enforcement has the ability to test DNA samples from crime scenes and upload the results into databases, like any other customer can, and it appears they have been doing it at other companies for the past year,” he said. “The distinction is that, according to our Terms of Service and Privacy Policy, we expect the FBI and law enforcement agencies to let us know when they submit something to our database.”

A company spokesman said late Monday that the F.B.I. is only able to see other DNA profiles on FamilyTreeDNA that share some of the same genetic profile. Users can disable the “matching” option in their account settings, which would prevent the F.B.I., as well as ordinary users, from seeing their information, the spokesman said.

“Unless a valid court order is issued, such as a subpoena or search warrant, with which FamilyTreeDNA would have no choice but to comply, there is no difference in the level of database access provided to law enforcement than to an ordinary user of FamilyTreeDNA,” the spokesman, Patrick W. Murphy, said in an email.

The F.B.I. declined to comment.

After Buzzfeed reported on the arrangement, genealogists revolted. Some discussed creating a petition to encourage FamilyTreeDNA to reverse its decision, while others threatened to delete their profiles.

“Not being upfront about what it wanted to do and quietly changing its terms with no notice to current customers is a big ‘no no,’” Rachel King, the founder of Toll Genealogy, a resource for genealogists, said in an email. “At the end of the day, this is valuable work. Anything that helps put a name to unidentified body, potentially enabling their loved ones to finally know what happened to them, is a good thing.”

More than 15 million people have submitted their DNA to companies like FamilyTreeDNA in recent years. While they represent a small fraction of all people, the pool of profiles is large enough to allow 60 percent of white Americans — the primary users of DNA sites in the United States — to be identified through the databases, according to researchers.