The FBI has agreed to pay $299,000 in a partial settlement over the agency’s investigation of an online antiwar magazine more than a decade ago.

But the federal magistrate who approved the settlement has also ruled that the FBI was authorized to look into the magazine, Antiwar.com, and its staff members’ writings because it had published a “watch list” of people the FBI was investigating after the terrorist attacks on Sept. 11, 2001.

The magazine’s founder and director said the ruling, which is not yet final, would subject political dissidents to future government investigations. He said the magazine had found the watch list on the Internet.

“It means that they can arbitrarily open up investigations of activist groups and journalists simply on the basis of what they have said publicly,” Eric Garris said Wednesday at the publication’s San Francisco office.

The FBI did not respond to a request for comment.

Antiwar.com, a self-described “anti-interventionist, pro-peace website,” was established in 1995 to oppose U.S. military action in Bosnia-Herzegovina and has been critical of U.S. policy in the Middle East. In 2011, the magazine obtained an April 2004 FBI memo, with portions blacked out, that appeared to recommend an investigation of the publication as a possible threat to national security.

After the magazine posted the memo and ran editorials criticizing the investigation, Garris said, at least three donors withdrew their financial support, explaining either that they didn’t want to be associated with an FBI target or that they feared coming under surveillance themselves. The publication had to reduce its staff and hasn’t fully recovered from the financial losses, he said.

The lawsuit filed in 2013 in San Francisco by Garris and editorial director Justin Raimondo sought records of the investigation and a ruling that the FBI had acted illegally.

The FBI agreed to turn over most of the records — which, Garris said, showed “nothing even remotely criminal or terrorist” — and will pay $299,000 to cover the magazine’s attorneys’ fees and legal costs. But U.S. Magistrate Jacqueline Scott Corley also ruled that the FBI’s investigation had complied with federal privacy law, which allows the government to keep records of individuals’ political actions and viewpoints only if they are part of “an authorized law enforcement activity.”

“The FBI was investigating whether the publication of the watch list on Antiwar.com posed a national security threat,” Corley said in a May ruling. “It makes sense that in conducting that investigation, agents would review public writings of the persons associated with the website,” such as Garris and Raimondo, she said.

American Civil Liberties Union lawyer Julia Mass, who represents the two journalists, said they have asked Corley to reconsider her ruling in light of newly obtained documents that, Mass said, cast doubt on the basis for the investigation.

“It’s critical that those protections of privacy against federal agencies compiling descriptions of people’s First Amendment-protected activities not get undermined by an overbroad view of legitimate law enforcement activity,” Mass said.

Bob Egelko is a San Francisco Chronicle staff writer. Email: begelko@sfchronicle.com Twitter: @egelko