First Jersey Securities Inc., the fast-growing brokerage firm, has obtained a federal court order halting a Securities and Exchange Commission fraud hearing set for today after the firm complained that the government agency lost all of the records necessary for the defense.

The records, some 22,000 pages, were contained in four filing cabinets and assorted boxes left in an SEC hearing room in the 41-story downtown New York federal building when earlier hearings adjourned two years ago, according to statements by First Jersey's president and majority owner, Robert E. Brennan, and the firm's lawyers in sworn affidavits filed in U. S. District Court here.

The records consisted of hearing transcripts, notes and documents, including original records of First Jersey stock transactions and outlines for cross examination of witnesses by First Jersey attorneys, according to the First Jersey affidavits.

First Jersey lawyer Lewis D. Lowenfels said in his affidavit that these records "are irreplacable documents vital to the defense of my clients and vital for the use of myself and my co-counsel during the trial."

On the basis of those affidavits, Chief Judge Clarkson Fisher granted a temporary injunction on Sept. 25 staying further SEC hearings into the activities of First Jersey until a further hearing set for Oct. 22.

It was a bizarre turn in the SEC's lengthy legal struggle with First Jersey, a securities brokerage firm formed in 1974 and now operating 23 offices nationwide, including an active Fairfax County branch.

The firm, which specializes in low-priced stocks of small companies, was accused by the SEC in a 1979 civil complaint of defrauding customers by manipulating stock prices in five separate instances between 1975 and 1978.

After nine months of testimony, the SEC hearings were interrupted midway in October 1980 as both sides began negotiating a possible settlement. In December 1980, Brennan and First Jersey tentatively accepted a proposed settlement with the SEC staff that would have barred him from any contact with the firm for six months, without an admission of violations by Brennan or the firm.

Brennan said in an interview that, although the SEC failed to prove its case in the initial hearings, he and the firm had accepted the proposed settlement to end the costly litigation. They then decided this summer to withdraw from the settlement and continue contesting the SEC complaint in order to defend the firm's reputation, according to Brennan.

Brennan today called the loss of the files "an outrage" because of the possibility that the case will be thrown out before his company has a chance "to vindicate ourselves."

"We have been subjected to many cheap shots and false allegations," he said in a telephone interview. "Just when it's our turn to come to bat, they lose our files."

SEC attorney Linda D. Fienberg declined comment, but said "We will respond fully" to First Jersey's charges in papers to be filed with the federal court here later in the month. The Oct. 22 hearing will be held here before Federal Judge H. Lee Sarokin.

According to the court papers here, hearings on the SEC complaint started on Nov. 20, 1979, before Administrative Law Judge David J. Markum, whose office is next to the 10th-floor hearing room. It soon became clear that the hearing would take "many months, if not years," said Lowenfels.

In defending First Jersey, Lowenfels said he and his fellow attorneys had "assembled an enormous volume of files" that eventually filled four multidrawer cabinets, several transfer files, suitcases, litigation bags, boxes and other recepticals, according to the affidavits. "We literally moved our office to the hearing room," said Brennan.

These files were too enormous to be moved every day, so SEC officials said they could be stored in the hearing room, which Lowenfels described as "the most convenient, sensible approach" for both sides since it "lessened the risk of trial delays" because needed documents were not on hand.

The First Jersey attorney said the hearing room was locked each night, and government security guards checked people entering and leaving the federal building. Only government employes had keys to the hearing room, and even First Jersey lawyers had to ask for the room to be opened so they could look at their files. Furthermore, they said it was impossible to take large packages from the building without authorization from a federal official. The First Jersey affidavits said there were no records that any files had left the building.

Mentioning that the FBI had offices there, Lowenfels said in his affidavit, "Certainly I believed, if the federal building was safe to house sensitive government records, it would be equally safe to house my, my co-counsels' and my clients' files."

In December 1980, two months after the hearings were recessed, a paralegal working for First Jersey, Alice Ferrigni Rooke, went to the hearing room to get the files in order and found they were missing. She said in her affidavit that she noticed either the hearing room or the corridor outside it was being recarpeted. She told an SEC attorney, Patrick Finley, who, according to her affidavit, reported it to Michael T. Gregg, the SEC's chief enforcement attorney in New York who is handling the First Jersey case.

When Lowenfels called Gregg, the SEC attorney said the files likely had been moved to the adjoining office of Administrative Law Judge Markum. Lowenfels said he asked Gregg to verify this next time the SEC attorney visited the 10th floor and, "If there was a problem, to let me know." Lowenfels said in his affidavit that he heard nothing until last Aug. 26, when he asked to see the files and was told " 'there might be some problem.' "

"I told Gregg that this was a bombshell to me," Lowenfels said.

Despite a search by the SEC, the files had not turned up by mid-September. Ten days later, the securities firm went to court to stop the hearing.