The Soviet Union charged yesterday that U.S. officials were keeping a former Soviet diplomat and his family from returning to Russia in "a flagrant violation of basic human rights."

In an unusual news conference, the third-ranking official of the Soviet Embassy here, Yevgeniy Kutovoy, accused the United States of holding Anatoly Bogaty, his wife and two sons "by force, against their will."

Bogaty, 43, was first secretary of the Soviet Embassy in Morocco when he "disappeared" on Sept. 22, 1982, Kutovoy said, and has been in the United States for at least three years.

On Sept. 15, Kutovoy said, Bogaty's wife, Larissa, phoned the Soviet Embassy, telling a duty officer that she and her family had decided to return to the Soviet Union and asking for help.

She left a Virginia phone number, he said, but when another embassy official tried to return the call "within hours, . . . the number was dead."

"The matter is so serious," Kutovoy said, that Soviet Foreign Minister Eduard Shevardnadze, in Washington at the time, raised the Bogatys' case in his talks with Secretary of State George P. Shultz.

Embassy officials also asked the State Department for a meeting with the Bogatys, Kutovoy said, but were told this week that the family does not want to meet with them nor return to their homeland.

A former CIA official who works with Soviet defectors said that Bogaty was almost certainly an intelligence officer, and speculated that he may be opposed to his wife's desire to return.

In the past, the United States has not blocked the return of a Soviet defector's spouse, most notably in the case of former United Nations official Arkady Shevchenko, whose wife went home when he defected in 1978.

While the Soviets charged that the State Department's refusal to arrange a meeting with the Bogatys violated the 1968 U.S.-Soviet consular convention, State Department officials insisted that the agreement does not allow either country's consulates access to their own citizens against their will.

State Department spokeswoman Phyllis Oakley said that the Bogatys "are free to go and come in contact {with} whoever they wish. The decisions on that are up to them."

She gave no information on the Bogatys' whereabouts, saying only that "this couple is in the United States."

Kutovoy charged that after the Bogatys' 1982 disappearance in Morocco, "it took two years for the American authorities to admit to the fact that these Soviet citizens were in the United States."

On that occasion, in September 1984, the State Department scheduled a meeting between the Bogatys and Soviet Embassy officials, he said, but canceled it the next morning, saying the Bogatys "had changed their minds."

"We would like to know for sure," Kutovoy said, appealing for a chance to meet with the family, "that it is the decision of the Bogatys to stay or to leave."

He announced that Moscow had decided that if Bogaty returns, he "will not be criminally prosecuted" and that the Bogatys "will be guaranteed the right to live and work in Moscow," as well as education for their teen-age sons.

The Soviet official acknowledged that Bogaty, as first secretary of the embassy in Rabat, "had access to intelligence information," but he stopped short of drawing a parallel to the case of KGB defector Vitaly Yurchenko, who slipped away from his CIA escort in a Georgetown restaurant and returned to Moscow in 1985.

Kutovoy raised another case, however, charging that Georgi Gindra, a Soviet tractor company export official who received political asylum in Milwaukee in August 1986, found it "very difficult to contact the embassy" when he changed his mind last November and decided to return.

Kutovoy stressed that in her Sept. 15 call, Larissa Bogaty said she could be reached at the Virginia number "if I am called to the telephone," which he suggested was a sign that she was being held.

Although Bogaty had told the embassy she was calling from the Richmond area, a C&P Telephone Co. official said the unlisted number, assigned in May, was located in Falls Church and was disconnected on Tuesday.

The same location, he said, has now been given a new number, also unlisted.