By Charlie Savage, New York Times

WASHINGTON — A federal judge has rejected a legal challenge to rules permitting FBI agents, when working on domestic criminal cases, to search emails written by Americans that the government has intercepted without a warrant in the name of gathering foreign intelligence.

In an 80-page opinion (pdf) that was issued in November and remained classified until being made public Tuesday, Judge Thomas F. Hogan, the chief judge of the Foreign Intelligence Surveillance Court, ruled that what critics call “backdoor searches” of messages by the FBI comply with both the Constitution and the FISA Amendments Act. That 2008 statute legalized a form of the government’s once-secret warrantless surveillance program.

Under the program, which the Bush administration started in 2001 to hunt for terrorists, the government may collect, on domestic soil and without a warrant, international emails and phone calls of noncitizens abroad, even when they communicate with Americans.

Hogan’s ruling is notable because some lawmakers want to require government agencies to get a warrant before searching the raw repository of emails for an American’s name or email address. Bipartisan majorities in the House have twice passed such a proposal in the last two years, and it is expected to be a central feature of a fight over legislation to renew the FISA Amendments Act, which is set to expire at the end of 2017.

The ruling was also the first time that the intelligence court has reviewed the surveillance program with contributions from an outside “friend of the court,” rather than hearing arguments from the government alone. The USA Freedom Act, enacted by Congress in June, encouraged the appointment of such a person to raise civil liberties concerns in novel or significant cases.

To perform that role, Hogan appointed Amy Jeffress, who was a national security aide to former Attorney General Eric Holder and is now a lawyer at the firm Arnold & Porter. She raised both statutory and constitutional concerns about FBI searches for ordinary criminal cases.

She wrote that this practice went “far beyond the purpose” for which the emails had been gathered under the FISA Amendments Act, which Congress justified as meeting the government’s need to acquire “foreign intelligence information.”

Hogan disagreed. He noted that Congress also included a provision in the main part of the FISA Amendments Act — sometimes called Section 702 — that permits the government to retain information from the warrantless surveillance program if it is “evidence of a crime.”

“It would be a strained reading” of the statute, he wrote, “to permit FBI personnel to retain and disseminate Section 702 information constituting evidence of a crime implicating a United States person for law enforcement purposes, but to prohibit them from querying Section 702 data in a matter designed to identify such evidence.”

Jeffress also argued that FBI queries intended to pull up private emails of Americans for ordinary criminal purposes “do not comply” with the Fourth Amendment, which bars unreasonable searches. She noted that agents are permitted to routinely look for emails by Americans that were incidentally collected without a warrant, even when the agents have only vague suspicions about someone and lack sufficient evidence to get a wiretap warrant.

Hogan disagreed with that argument as well. He cited several rationales for permitting such queries, including the idea that a search for criminal evidence might bring up information that also proved useful for national security purposes.

The judge wrote that the Justice Department had told him that FBI queries intended to bring up messages that might be evidence of ordinary crimes “rarely, if ever” return useful information, so “the court is not prepared to find a constitutional deficiency based upon a hypothetical problem.”

However, he ordered the government to begin reporting to the court every time an FBI agent working on an ordinary criminal matter searched the database for an American suspect’s private messages and ended up reading some of them.

Hogan also approved several modifications to the rules for the program that the Privacy and Civil Liberties Oversight Board, an independent watchdog agency, had suggested after reviewing the program.

They include requiring officials who search for Americans’ emails for a national security purpose — including analysts at the National Security Agency and the CIA — to document in writing why they believed they were likely to find information related to foreign intelligence. (Jeffress did not quarrel with permitting searches of Americans’ emails for that purpose.)

A separate part of the judge’s opinion, which was heavily redacted in places, scolded the NSA and the FBI for instances in which they violated court-imposed rules for the program. The violations appeared to involve a failure to purge cellphone calls collected without a warrant after a foreign target had “roamed” onto domestic soil, as well as a failure to set up special teams to review the communications of foreign targets who had been indicted, in order to screen out any information protected by attorney-client privilege.

But while Hogan wrote that he was “surprised” and “extremely concerned” about the problems — which the government said it was fixing — he said they were not a reason for him to withhold approval of the program for another year.

In another previously classified opinion made public Tuesday, Hogan, in a ruling issued late last year, approved the first querying of a newly created system for analyzing links between callers in search of hidden associates of a suspect in a national security case.

That new system, which was also established by the USA Freedom Act, searches bulk data held by the telephone companies. It replaced a once-secret program in which the NSA had systematically collected Americans’ domestic calling records in bulk.

To Learn More:

            Memorandum Opinion and Order (U.S. Foreign Intelligence Surveillance Court) (pdf)

Director Comey Admits FBI does Conduct Surveillance without a Warrant (by Noel Brinkerhoff and Danny Biederman, AllGov)

NSA Collects and Stores Web History of Millions of Users, Creates Profiles of U.S. Citizens (by Noel Brinkerhoff, AllGov)

FBI Wants More Authority to Spy Live on Gmail, Skype, Dropbox and Cloud (by Matt Bewig, AllGov)