Justice department prosecutors took the unusual step on initiating plea bargaining with former Central Intelligence Agency Director Richard M. Helms, in part because they feared that top-secret information might be disclosed if Helms brought to trial.

Benjamin R. Civiletti, head of the department's Criminal Division, said in an interview that seeking a plea by Helms on misdemeanor charges was the "safest way" to safeguard the principle that not even the nation's top intelligence officer "is above the law."

Helms pleaded "no contest" Monday to two misdemeanor criminal charges for failing to testify fully and accurately to a Senate committee about CIA's activities in Chile.

In a briefing for reporters yesterday, both Civiletti and Attorney General Griffin B. Bell strongly rejected any suggestion that the plea could be interpreted as giving intelligence officials a license to lie.

"It means just the opposite." Bell said. "We've gotten someone to plead to a criminal violation . . . It sets the nation on a new course."

Civiletti added: "We thought it was vital that there be a prosecution [to show] that no segment of the community was above the law."

The idea of plea bargaining was first discussed with President Carter. Vice President Mondale and national security adviser Zbigniew Brzezinski at the White House in late July, Bell said. It is considered rare for a prosecutor to initiate plea bargaining.

At a first meeting in early September, Helms' attorney, Edward Bennett Williams argued forcefully that the case be dropped, Civiletti said.

He said that Williams never threatened that the names of other prominent individuals such as former Secretary of State Henry A. Kissinger would be brought up during a trial. But Civiletti added, "As a good lawyer it is clear that he would want to develop theories of defense that would result in wideranging discovery proceedings."

And Bell said that if classified documents uncovered in those proceedings were ruled admissible, "we might have to abort in the middle of a trial."

This concern about national secrets, plus the risk that a jury might agree with Helms' defense that he could not testify fully because of his CIA oath against disclousure were factors of the decision to plea bargain, according to Civiletti.

Both he and Bell said they never considered asking Helms to plead to a felony charge, such as perjury, because they were sure he would flatly reject such a deal."That wouldn't have been a bargain [for Helms]," Bell said.

"It doesn't matter a helluva lot whether the plea is to a misdemeanor or a felony." Civiletti said. "What matters is achieving the principle of being accountable to the law while eliminating the risks."

At the White House yesterday, deputy press secretary Rex Granum said that the decision in the Helms case was "consistent" with President Carter's campaign statements that equal standards of justice should apply to both ordinary citizens and prominent persons, including "Washington big shots."

Civiletti said he laid out the department's evidence against Helms in a Sept. 20 meeting with Williams and argued that some plea was necessary in the case.

On Oct. 11, he said, Williams came back to him with a set of conditions that included an understanding that there would be no jail sentence for Helms, and a request that Helms' federal pension be left intact.

The final agreement was reached in meetings last week, but the whole arrangement almost fell through when U.S. District Court Judge Barrington D. Parker refused Monday to automatically accept the "no jail" provision!

Bell and Civiletti both citd the delicate nature of the plea-bargaining arrangement as the reason they arranged to have the court session Monday conducted in near secrecy. The two-count information against Helms was sealed when it was filed Monday morning and Civiletti said he met with the judge and Williams three times privately before the plea was finally taken in open court that afternoon.

Civiletti noted that the department's investigation of U.S. activities in Chile is continuing, apparently focusing on the actions of officials of International Telephone and Telegraph Corp. in any future trials, he added. Helms may be a government witness.

The CIA operation in Chile in 1970 was aimed at preventing the election of Salvador Allende as president. ITT officials are alleged to have a aided Allende's political opponents in that campaign.

It was about these events that Helms agreed in court on Monday that he had testified less than candidly.