Among the controversies aroused by New York Times reporter M.A. Farber's refusal to surrender his notes to a New Jersey judge is the argument that Farber somewhere stepped across the bounds that should govern a reporter and became an agent of the government.

"This man is not a reporter, he's an investigator," defense attorney Raymond A. Brown told the New Jersey Supreme Court in making his charge against Farber.

New Jersey Attorney General John Degnan noted that the Farber case, in which freedom of the press claims collide with a defendant's efforts to assert his right to a fair trial, has become overhung with talk of "a grand conspiracy" between Farber, The New York Times and the prosecution.

Degnan went on to point out that there has been no courtroom examination of this conspiracy claim. "The court ought to look at it," he said, because the alternative is a subpoena for every reporter's file in every criminal case.

Talk of a conspiracy begins with Brown, the defense attorney who subpoenaed Farber's notes in an effort to aid the defense of his client, Dr. Mario Jascalevich, against charges that the doctor murdered three patients in an Oradell, N.J., hospital by injecting them with lethal doses of curare, a muscle-relaxant.

Conspiracy or not, Farber's role became central to the case because without him there would have been no indictment and no prosecution of Jascalevich.

In Farber's first story about the case, Jan. 7, 1976, he quoted prosecutor Joseph Woodcock Jr. saying: "The facts presented as a result of the Times inquiry and as a result of our own study of the official file require that we reopen the case."

"This thing had been batting about [Bergen] County for some time," Bergen County Medical Examiner Dr. Lawrence Denson recalled. "It was the sort of thing people talked about at cocktail parties."

For all the cocktail party conversations, nine years had passed since a series of unexplained deaths at the Oradell hospital, and the official file had been long closed when Farber began to look into it.

His first information came in an unsolicited letter to the Times from Eileen Milling, a New York public relations woman who claimed 30 to 40 patients had been murdered in "a case of a warped mind playing chess with other people's lives."

Because Farber had done a number of stories about medical mysteries, his editor passed Milling's June 20, 1975, letter to him.

Farber was involved in another story that took up most of his time, but he made enough inquiries to learn the suspected murderer's name and the hospital where the deaths had taken place in 1965-1966.

It wasn't until late August, however, that Farber's interest was further increased by a story reporting an outbreak of similarly mysterious deaths in Ann Arbor, Mich.

The Ann Arbor story triggered two developments in Bergen County.

Detectives reminded prosecutor Woodcock (who had not been in office at the time of the deaths) of the Oradell file resting in a warehouse, and they decided to dig it out in case the FBI wanted it in connection with the Ann Arbor investigation. In addition, Farber went to see Woodcock for the first time.

The prosecutor agreed to give Farber access to the large file, and an arrangement was made for the reporter to examine it in a government office after signing for it.

"The file," Farber said, "made all the difference in the world." The Missing Deposition

AT THE ROOT of Brown's allegation that Farber became transformed into an arm of the prosecution are the circumstances surrounding a deposition of Jascalevich taken in 1966 by the prosecutor at that time, Guy Calissi.

Farber noticed that the file contained depositions of several doctors from Riverdell Hospital in Oradell, but none of Jascalevich.

In September, now working full-time on the story, Farber contacted Matthew Lifflander, a New York attorney who, at the instigation of Dr. Alan Lans, one of the owners of Riverdell Hospital, had sought to keep the original 1966 investigation of the deaths alive.

Farber mentioned the missing Jascalevich deposition in passing, Lifflander recalls, and the lawyer said: "Hey, I've got that."

What Lifflander had was a copy of the deposition that prosecutor Calissi had given him along with some slides ofn tissue from some of the dead. Lifflander had taken them to New York City's medical examiner, Dr. Milton Halpern, in the hope that Halpern could come up with evidence that would advance the investigation.

Farber gave a copy of the deposition to Woodcock to fill out the prosecutor's file, and the deposition was key to persuading Woodcock that there was sufficient reason for him to reopen the investigation that had lain dormant for nine years. There is no statue of limitations on murder in New Jersey.

At the murder trial last week, Woodcock testified that the Jascalevich deposition was the only thing Farber gave to his office.

Ironically for Farber, the original of the Jascalevich deposition was located in the home of Fred Galda, who had been Calissi's chief assistant at the time of the original investigation and had taken it because, although no indictment was brought, he found the case so fascinating that he had considered writing a book about it. Farber has been severely criticized by Federal Judge Frederick Lacey and defense attorney Brown because he has a contract to write a book about the case.

Calissi and Galda have both become judges of the Superior Court, the court in which Jascalevich's murder trial and Farber's contempt conviction have been handled by other judges. The Tape Machine

FARBER SPENT 26 days in jail and the Times paid $110,000 at the rate of $5,000 a day as a result of their being found in contempt for refusing to give his notes to trial judge William Arnold. Arnold had ordered them submitted to him so that he could determine whether they should be made available to Jascalevich to aid his defense.

In their refusal, Farber and the Times said Jascalevich's subpoena was an overly broad fishing expedition since it did not specify what sort of information he was seeking, but demanded all Farber's material.

Farber's lawyer, Floyd Abrams, made clear before the New Jersey Supreme Court that Farber is ready to surrender certain parts of his private files. Abrams said this was not a retreat from Farber's and the Times' initial position, but was simply the first time they had a courtroom opportunity to clarify their positions.

Farber's discovery of the missing Jascalevich deposition not only led to the reopening of the investigation of Jascalevich, but ended Farber's access to the official file on the case.

Woodcock denied him further time with the file on the grounds that the investigation was no longer ancient history.

Before he lost his access, Farber took another action that Brown has raised as evidence that he was behaving as more than a newspaper reporter.

The file contained belts from an old-fashioned recording device that could not be heard because Bergen County no longer had a machine of their type.

Farber searched for the right machine and found one in a New York store which he took to Bergen County. However, the machine didn't work and Farber didn't hear the tapes, parts of which have since been played at the Jascalevich trial.

A third question about Farber's role arises from the way he signed in on the prosecutor's log of visitors when he went to read the file. On at least one occasion, Farber wrote the word "official" in the space headed "purpose of visit." Farber says he agreed with Woodcock that he wouldn't identify himself on the log as a Times reporter because he didn't want other reporters who cover the courthouse daily for New Jersey newspapers to know he was looking into a case.

Brown has also raised questions about the relationship of Woodcock, Farber and the present New York City medical examiner, Dr. Michael Baden. Farber consulted Baden and a number of other experts as he researched his story. After Woodcock reopened the Bergen County investigation, he also turned to Baden for advice on whether curare could be found in the bodies should they be exhumed so many years after death.

In court last week, Brown asked Woodcock whether Farber had brought him together with Baden. Woodcock said he did not remember who introduced him to Baden but was quite sure it was not Farber. Who Was Aiding Whom?

THE QUESTION about the Farber-Woodcock relationship is: Who was aiding whom? A lot of reporters have asked prosecutors for access to their files. Not many reporters have found gaps in a prosecutor's file and filled them.

"We weren't looking at that file. It was as unknown to me as a Dead Sea Scroll," Woodcock said of his first contacts with Farber.

"Farber did what I think is the role of any reporter - to investigate and take it where it goes. In this case, it led to a prosecution," he said.

Farber says flatly: "This story would never have been written without my penetration of that file."

What if Farber had found the missing deposition and instead of giving it to Woodcock had kept it in his private files? Would judges have looked with favor on a reporter who claimed that an official deposition had become his property and that the office which took the deposition had no right to a copy?

No one has accused Farber of working on the Jascalevich case without having as a goal publication of stories in the Times.

No one disputes that without Farber's investigation the mysterious deaths at Riverdell Hospital would have continued to be nothing more than a topic of conversation among doctors and lawyers in Bergen County.

In the experience of Farber's lawyer, Abrams, who has handled many press cases, the allegation that a reporter has lost his constitutional protection because he functioned as an agent of one of the parties to a lawsuit is new.

If investigative reporters are construed to be working for any party to a law case that their work aids, most investigative reporters can be seen by someone or other as an agent of someone or other, Abrams said. "And that would be very dangerous."