A former FBI supervisor was indicted by federal grand jury yesterday on charges of directing a secret mail-opening and wiretapping operation during a search for radical fugitives in New York City from 1970 through 1972.

The five-count indictment against John J. Kearney, a retired special agent, marked the first criminal charges to come out of the Justice Department's year-long probe into the FBI's use of illegal burglaries, wire-tapping and mail tampering against political militants in the early 1970s.

Kearney, 55, retired from the FBI in 1972 after heading a special intelligence unit in the New York field office known as Squad 47. The unit was responsible of pursuing fugitive members of the Weather Underground charged with bombings and other terrorist activities.

His indictment appears to represent the first step in a Justice Department drive to prosecute several present and former high-ranking FBI officials for their roles in allegedly ordering and covering up the burglaries.

Attorney General Griffin B. Bell is known to have received a recommendation last week that the department try to get at these higher-ups by seeking indictment of those in middle-level supervisory positions at the time of the burglaries.

Department sources said this strategy is a long shot that carries no guarantees of success in eventually winning indictment of six or more FBI executives who are the main targets of the probe. The hope, the sources said, is that indictment of lower-level figures will trigger the plea bargaining, testimony and evidence required to prosecute the higher-ups.

Department spokesmen yesterday would say only that the "investigation is continuing" and refused to speculate about whether there would be other indictments. However, other department sources said they considered Kearney's indictment a "clear sign" that Bell has decided to pursue further prosecutions.

FBI sources said Kearney is the first agent ever indicted for allegedly committing a crime in the course of his official duties. Last summer, a Justice Department investigation into financial irregularities within the bureau resulted in the resignation of John P. Dunphy, head of the FBI's exhibits section. He avoided indictment by pleading guilty to a misdemeanor charge involving use of government lumber to build a birdhouse at his home.

Yesterday's indictment, returned in U.S. District Court in Manhattan, charged Kearney with two counts of conspiracy, two of obstructing correspondence and one of illegal wiretapping.

If convicted, he would face sentences of up to five years' imprisonment and a $10,000 fine on each conspiracy and wiretap charge and five years' imprisonment and a $2,000 fine on mail-opening charges.

The indictments alleges that Kearney organized and directed a covert operation that became known in the New York field office as the "mail run." Under his direction, the indictment charges, FBI agents removed letters from private mailboxes at various New York addresses, took the letters to their office, opened them with a device called a steamer, read and copied the contents and then returned the mail to the boxes.

In addition, the indictment continued, Kearney directed agents in 11 wiretaps on the telephones of persons suspected of having contacts with Weatherman fugitives. All of these taps were carried out illegally without court authorization, the indictment said.

The indictment did not identify the fugitives being sought by the FBI. However, they are believed to have included Mark Rudd and Bernardine Dohrn, prominent Weatherman leaders missing since a 1969 vandalism binge by leftist demonstrators in downtown Chicago known as the "Days of Rage."

Among those listed as targets of the wiretaps and mail openings was Jenifer Dohrn, believed to be a relative of Bernardine Dohrn. The indictment listed 24 persons, all believed to be relatives or friends of fugitives, as targets of the illegal FBI surveillance tactics.