A New Jersey judge yesterday sentenced a New York Times reporter to jail for at least six months and fined his newspaper a minimum of $100,000 for their refusal to surrender the reporter's notes on a murder case.

Reporter M.A. Farber was taken into custody at the Bergen County Jail immediately after Superior Court Judge Theodore Trautwein found him and The Times guilty of civil and criminal contempt.

Trautwein ordered Farber jailed until he surrendered his notes and fined him $1,000 on the civil contempt charge. On the criminal contempt charge, Farber was fined an additional $1,000 and sentenced to six months jail, with that sentence to begin after he turns over his notes. The judge fined The Times $5,000 a day until the notes are surrendered on the civil charge and $100,000 on the criminal charge, payable today.

Lawyers for The Times appealed Trautwein's judgement to the New Jersey Court of Appeals and Times Publisher Arthur O. Sulzberger issued a statement defending Farber's decision to preserve the confidentiality of his sources.

"This is what a free press is all about,"Sulzberger said. "And if Judge Trautwein decrees that The Times is to pay $5,000 a day for this privilege, so be it. Bad law doesn't last very long."

In a statement after the judge's order, Farber said: "I gave my word that I would respect these confidences, and I gave it in what I believe to be the public interest. I am a custodian of that word today as yesterday."

Farber and The Times were charged with civil contempt when the reporter refused to honor a subpoena in the case of Dr. Mario Jascalevich for Farber's notes, which the doctor believes are vital to his defense against charges he murdered five patients at an Oradell, N.J., hospital by giving them lethal doses of curare, a powerful muscle relaxing drug.

Farber's investigation of a series of mysterious deaths at the hospital in 1965 and 1966 helped reopen the investigation of those deaths, resulting in the indictment of Jascalevich.

The criminal contempt charges were brought when Farber and The Times refused a court order to turn the reporter's files over to Bergen County Judge William Arnold so that Arnold could determine whether they should be given to the defense.

The longest jail term an American reporter has served for preserving the confidentiality of his sources was the three months served by Mark Knops, a reporter for The Madison, Wis., Kaleidoscope. Knops was jailed after he refused to disclose to a grand jury the sources of statements from radicals claiming responsibility for the 1970 bombing of the Army Mathematics Research Center at the University of Wisclonsin.

In his statement, Farber declined: "There is nothing in my notes that would establish the defendant's guilt or innocence for the trial court, and there is certainly nothing that would leand credence to his theory that he is being framed."

His decision to defy the subpoena, Farber said, was based on the right of the public to be informed by the press in accordance with the First Amendment.

"The inevitable result of my compliance with this order would be my conversion into an investigative agent for the parties to this case," Farber said. "And, most important, I will have given notice that the nation's premier newspaper is no longer available to those men and women who would seek it out - or who would respond to it - to talk freely and without fear."

Farber has already appeared as a witness in the Hackensack, N.J., trial of Jascalevich. He answered some questions, but refused to reply to others, saying he would not reveal condidential sources. Faber cited both the Constitution and New Jersey's shield law as grounds for his refusal.

The reporter began his investigation of the deaths at the Oradell hospital in early 1976, about 10 years after they occurred. The bodies of five of the 13 patients who had died mysteriously were exhumed for the reopened investigation.

The prosecution alleges that Jascalevich murdered the five patients in order to make their doctors appear incompetent and thereby enhance his own power at the hospital.

There has been testimony that Farber showed the prosecutor a copy of a statement by Jascalevich that had been missing from the prosecutor's file, and that the statement was instrumental in the prosecutor's decision to reopen his investigation.

At an earlier stage in the trial, which has been underway for more than 21 weeks, Judge Arnold said that Farber should shoulder the responsibilities of an investigator if he had played the role of an investigator aided the prosecution.

If appeals by Farber and The Times fail, the daily penalty in the civil contempt action would end at the conclusion of the Jascalevich murder trial.