Two Soviet employes at the United Nations were arrested yesterday by the FBI on espionage charges that they paid $16,000 for secret Navy antisubmarine warfare documents.

A third Russian citizen, attached to the Soviet mission at the U.N., was also picked up by FBI agents but was not charged because he has diplomatic immunity, a spokesman for the Federal Bureau of Investigation said.

The three men were taken into custody yesterday afternoon in a Woodbridge, N.J., shopping center shortly after an unidentified U.S. Navy officer - who had been cooperating with the FBI - dropped off a roll of film in an orange juice container.

The espionage arrests were the first of Russians in the United States since a 1972 case involving an earlier Soviet U.N. employe who allegedly received plans for a new U.S. Navy fighter plane, the F14. Charges against Valerily I. Markelov were dropped and he left the country.

Yesterday's arrests seem certain to heighten strained relations between the United States and the Soviet Union.

Attorney General Griffin B. Bell told President Carter about the case, a Justice Department spokesman said. But a spokesman for the National Security Council said he was not aware of the case or any high-level discussions about the implications of going forward with prosecutions.

The two men charged in the case, Rudolf P. Chernyayev, 43, a U.N. personnel officer, and Valdik A. Enger, 39, an assistant to the U.N. under secretary general, were considered international employes of the U.N. and thus have no diplomatic immunity, an FBI spokesman said.

Arkady Shevchenko, a high-ranking Soviet career diplomat at the U.N., recently sought political asylum in the United States but had nothing to do with the investigation leading to yesterday's arrests, the spokesman said.

The third Soviet, named a co-conspirator in a complaint filed as the basis for arrest warrants, was identified as Vladimir P. Zinyakin, 39, an attache at the Soviet U.N. mission.

A State Department spokesman said yesterday that a minister counselor at the Soviet embassy in Washington was called in yesterday to hear a U.S. protest about the involvement of the three Soviets in the alleged espionage.

Though Zinyakin has diplomatic immunity and was released from custody yesterday, the Soviet embassy official was informed, the spokesman said, that Zinyakin's departure from the United States is expected because he violated his status.

According to the complaint, the key to the case was the Navy officer who cooperated with the FBI and the Naval Investigative Service since he was first contacted last August. Authorities refused to identify the American officer yesterday, though he is certain to be the star witness for the prosecution in any trial.

The 13-page complaint outlines a sophisticated scheme in which the Navy officer never had a face-to-face meeting with alleged spies. Instead, the alleged Russian spies made a series of calls to phone booths along New Jersey turnpikes to direct the American to other locations for pickups of instructions and money drops of films of classified documents.

The complex plans were finally penetrated, however, according to the charges, because the Navy officer tipped off the FBI and agents observed the Soviets driving to the pickup spots in cars registered in their own names.

After the first contact with the American last August, the complaint said, he was asked to obtain secret information about antisubmarine warfare, including materials involving underwater acoustics and submarine detection systems such as a sub-hunting helicopter.

Antisubmarine warfare is an area in which the United States has a significant lead over the Soviets and is thus a logical target for espionage.

The United States has microphones lying on the ocean floor constantly tuned to Soviet submarines sailing off American shores. This detection system is so sophisticated that a computer can figure out from the detected sound exactly which submarine is out there. Each submarine has a distinct sound "signature."

The U.S. listening system also plots the speed and course of Soviet submarines which are otherwise invisible. Knowing the location of a submarine is the key to destroying it with modern torpedos if war should come.

In addition, the United States has made big advances in recent years in finding submarines through devices dropped from aircraft and towed behind ships at various depths. And the United States also has top secret equipment on its own subs designed to kill Soviet subs in wartime.

The Navy has an antisubmarine warfare base at the former drigible port in Lakehurst, N.J., easy driving distance from the drop point, although it is not known whether the officer was stationed there.

On one occasion cited in the FBI complaint, the American officer - known as "Ed" - said he waa called at a prearranged public phone along the Garden State Parkway by his contact "Jim." He was told to find instructions hidden under the shelf of a nearby phone.

After doing so, he followed the orders to a drop site at the "base of the third telephone pole on Fulner Street in South Amboy, N.J." There he dropped off a milk carton containing his film and picked up a red coffee can, the complaint said.

In the can was $3,000 and a type written letter from "Jim" which said in part, "Please try to prepare material on submarine acoustic detection system" for the next drop.

Staff writer George C. Wilson contributed to this report.