Journalist Judith Miller and U.S. Attorney Patrick Fitzgerald squared off in court again yesterday, with a lot less public attention than last year, when the dogged special prosecutor in the Valerie Plame case had the then-New York Times reporter jailed for 85 days to force her to disclose the identity of an anonymous source.

Yesterday appearance in Manhattan before the U.S. Court of Appeals for the Second Circuit was another instance of Mr. Fitzgerald trying to find out about Ms. Miller’s sources, this time by looking at the New York Times’s phone records, and prosecutors raised the prospect of pressing her directly yet again, as they did in the Plame case to disclose the sources.

At the center of this leak case is the question of how Ms. Miller, who has since left the paper, and a second Times reporter came to learn of the government’s plan to take action in the wake of September 11 against two Islamic organizations suspected of having terrorist ties.

The government is appealing a ruling by U.S. District Judge Robert Sweet last year that barred Mr. Fitzgerald from inspecting Ms. Miller’s phone records. Mr. Fitzgerald’s appeal has come before judges Amalya Kearse, Robert Sack, and Ralph Winter of the Second Circuit of the U.S. Court of Appeals. Judge Winter was absent from the panel at yesterday’s hearing.

Mr. Fitzgerald, present yesterday as the U.S. Attorney for Northern Illinois, did not address the court.

He left the arguments to another federal prosecutor, James Fleissner, who warned that Judge Sweet’s ruling to protect journalist phone records may encourage investigators to more regularly question reporters themselves about their sources.

That warning suggests that federal prosecutors could be influenced by that 2005 ruling, which is understood as offering significant First Amendment protection for reporters, to be even more willing to question reporters directly instead of going through phone companies to learn of their sources.

In March 2005, Judge Sweet ruled that the government had not demonstrated that there were no alternative sources besides the phone records of the two reporters that would allow the investigation to proceed.

“This may be a case of be careful what you ask for,” Mr. Fleissner said in court yesterday. “What that means is we should have subpoenaed the reporter directly.”

Mr. Fleissner argued on behalf of the government that using phone records to identify a reporter’s source is less intrusive than demanding that a reporter answer questions before a federal grand jury.

“The government acted on the premise that it’s a lesser step,” Mr. Fleissner said after court of the government’s decision in the present case to seek records from the phone company rather than questioning reporters directly.

An attorney representing The New York Times, Floyd Abrams, rejected that argument. Mr. Abrams has called the government’s request for weeks of phone records “overbroad” and said it would reveal the identities of dozens of sources of Ms. Miller and the second New York Times reporter involved, Philip Shenon.

“Telephone records are the extension of the journalist herself,” said Mr. Abrams, arguing that telephone records deserve protection under the First Amendment. “Telephone records are the embodiment of the speech of the journalist.”

Judge Sack, who served as a lawyer for publisher Dow Jones before being named to the bench by President Clinton, signaled that he was critical of Mr. Fleissner’s argument. He questioned whether using Mr. Fleissner’s argument would permit investigators to “then go in and subpoena the surveillance camera” of a location where a reporter was believed to have met with sources.

Ms. Miller, who was present in court and following the attorneys’ arguments with a notepad in hand, told The New York Sun after the court that her departure from The New York Times following her release from jail does not affect the Times’s effort to protect her phone records. Mr. Shenon was not present in court Monday.

During the court proceedings, Mr. Fleissner called the subpoena “unusual but not unprecedented and unique.” He argued that the case should never have been heard originally in Manhattan, where the New York Times is headquartered, but in Illinois, where the investigation is based. The Times went into court in New York in the case in what some experts said was an effort to gain a more favorable venue.

Nonetheless, Mr. Fleissner’s warning to “be careful what you ask for” was viewed by some as a possible outline of how the government would proceed in future leak investigations.

“On a broader level it is a threat,” Mr. Abrams said. “What he’s saying is if you win maybe we will stop following a Mr. Nice Guy path. That is to say, maybe we won’t go after phone records, we’ll go after the journalists.”

In at least five ongoing cases federal grand juries have issued subpoenas to journalists in cases relating to their reporting or courts have ordered journalist to give up sources, according to a list kept by the Reporters Committee for Freedom of the Press.

The phone records in question would likely show who told Ms. Miller and Mr. Shenon that the government planned to freeze the assets of the Islamic charities Global Relief Fund and the Holy Land Foundation for Relief and Development, Judge Sweet’s ruling states. Ms. Miller had been reporting on links between terrorism and Islamic charities for years before her story on the Global Relief Fund was published in 2001.

Mr. Fitzgerald has alleged that Times reporters tipped off the Global Relief Foundation and the Holy Land Foundation before December 2001 searches, thus compromising the actions. Both charities are accused of ties to Islamic extremist terrorists.

The case is New York Times Company v. Gonzalez.