A media organization in the Bay Area sued the Trump administration Wednesday over its seizure of phone and email records of a New York Times reporter who, during a relationship with a Senate Intelligence Committee aide, unearthed a Russian attempt to recruit a future Trump campaign adviser.

The reporter, Ali Watkins, was working for other news outlets during her three-year relationship with Senate staffer James Wolfe, who was charged by the Justice Department in April with lying to the FBI when he denied giving classified information to reporters. He has pleaded not guilty.

The lawsuit, filed by the First Amendment Coalition in San Francisco federal court, seeks an explanation from the Justice Department for its failure to notify Watkins before obtaining six months of her phone records and up to two years of her emails from telecommunications providers. The seizure of the records was reported publicly in June.

Government acquisition of journalists’ personal, confidential records “threatens the ability of reporters to carry out their mission, enshrined under the United States Constitution, to report on matters of public interest and to hold the government accountable,” lawyers for the media organization, based in San Rafael, said in the suit.

They said it was the first reported seizure of journalists’ records by the Trump administration.

The Justice Department did not respond to a request for comment.

Watkins reported in April 2017, while working for the online media company BuzzFeed, that Carter Page, a foreign policy adviser to Donald Trump’s presidential campaign, had provided documents in 2013 to a Russian intelligence agent, who tried to recruit Page to work with Russia. Special Counsel Robert Mueller has been looking into Page’s contacts while investigating possible Russian interference in the 2016 election.

The Times hired Watkins last December, but later learned of her past relationship with Wolfe, a relationship that is at odds with conflict-of-interest standards followed by most news organizations. The newspaper reprimanded her and transferred her from Washington to New York, under a mentor’s supervision.

Wednesday’s lawsuit cited guidelines adopted by President Barack Obama’s attorney general, Eric Holder, in 2015 after an uproar over the FBI’s secret subpoena for phone records of Associated Press and Fox News reporters. The guidelines, later adopted as federal regulations, instructed the department to notify news organizations before seeking such records, and give them a chance to object, unless there were compelling reasons to act in secret.

The First Amendment Coalition said it contacted the Justice Department in June, under the Freedom of Information Act, asking why Watkins had not been contacted before her records were seized, and filed suit when there was no response.

David Snyder, the coalition’s executive director, said the information would enable the public to understand “when, how and why the (Justice Department) is collecting records of journalist communications — and if they are overreaching in doing so.”

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