The New York Times suffered a legal setback yesterday in its battle to keep a federal prosecutor, Patrick Fitzgerald, from obtaining the phone records of its former reporter, Judith Miller.

A federal appeals court yesterday granted the government access to newsroom phone records as part of an investigation into how two Islamic charities were tipped off to impending FBI raids.

The 2-1 decision reverses a lower court ruling and upholds the subpoenas for the phone records from late 2001 of two reporters, Ms. Miller and Philip Shenon. Because prosecutors sought the records from a telephone company — and not from the Times — the ruling does not demand any compliance on the part of the newspaper. In an unrelated 2005 case that involved the same federal prosecutor, Ms. Miller spent 85 days in jail until she agreed to testify in the Washington, D.C., case relating to leak of CIA agent Valerie Plame’s identity.

In the current case, the Times had argued that the First Amendment freedom of the press should prevent the government from examining the phone records of its reporters. The disclosure of those records would reveal the identity of dozens of confidential sources, both reporters say in affidavits.

The ruling, written by Judge Ralph Winter of the 2nd U.S. Circuit Court of Appeals, holds that because the case involves an alleged tip-off, the reporters are not entitled to the extra protection often afforded to the press under the First Amendment.

The case entered the courts in 2004, when the Times learned that prosecutors from Chicago were seeking records of phone calls that Ms. Miller and Mr. Shenon had made during several weeks in 2001 — around the time they published stories on two Islamic charities with suspected ties to terrorists, the Holy Land Foundation and the Global Relief Foundation. Prosecutors, led by the U.S. Attorney for the Northern District of Illinois Patrick Fitzgerald have claimed that the two reporters had tipped off the groups about impending raids and of the government’s decision to freeze their assets. The government has said the phone records are relevant to a grand jury investigation into who inside the government had originally tipped off the reporters.

The Times has maintained that the reporters did nothing beyond routine reporting.

“We see no danger to a free press in so holding,” Judge Winter writes of the decision to allow the government access to the records. “Learning of imminent law enforcement asset freezes/searches and informing targets of them is not an actively essential, or even common, to journalism. Where such reporting involves the uncovering of government corruption or misconduct in the use of investigative powers, courts can easily find appropriate means of protecting the journalists involved and their sources.”

The dissenting judge, Robert Sack, chides the majority in his 38- page dissent for finding that the alleged facts deny the two Times reporters the protections under the First Amendment afforded to journalism.

But Judge Sack — who was a lawyer for publisher Dow Jones before being appointed to the bench by President Clinton — also questions the government’s need for the phone records and the extent of prosecutors’ efforts to trace the leak before demanding the phone records.

Citing the slow the slow pace with which the government has tackled this leak case, Judge Sack writes: “the elapsed four and a half years does fairly raise the question of just how significant the leaks were or are considered to be by the government.”

The majority opinion, which the third judge on the panel, Judge Amalya Kearse, signed, grants one significant victory to news organizations. It holds that reporters have standing to challenge the government’s efforts to obtain phone records from a third party in a separate court proceeding. Originally the government had maintained that its subpoenas required no other review than from the judge presiding over the grand jury proceeding.

This aspect of the majority decision drew the praise of Judge Sack, the dissenter, who wrote that without that protection reporters might be forced to communicate in the manner of drug dealers — “by use of clandestine cell phones and meetings in darkened doorways.”

An in-house lawyer for the paper, George Freeman, told The New York Sun following the ruling that the paper was “considering its options.” An appeal would involve requesting that the entire 2nd U.S. Circuit Court of Appeals review the case.

“The notion of doing business in a park where there’s not the trail of whom they talked to becomes more real,” Mr. Freeman said of the potential impact of the ruling on journalists.

Floyd Abrams, the celebrated First Amendment lawyer with Cahill, Gordon & Reindell who argued the case, did not return a call for comment. Judge Winter, who wrote the majority opinion, was not present on the snowy day in February that the case was argued, but apparently saw a transcript of the proceedings.

Government requests for phone records from news organizations are rare, several lawyers familiar with the case said.

A spokesman for the U.S. Attorney’s office for the Northern District of Illinois declined to comment on the decision or answer questions regarding the status of the leak investigation.

The decision reverses a ruling by Judge Robert Sweet of U.S. District Court in Manhattan who ruled last year that the reporters had a qualified privilege under the First Amendment to maintain the confidentiality of their records.

The case is New York Times v. Gonzales. The Times initiated the case in New York, in what some thought was an attempt to get a friendlier set of judges than it might get in Illinois.