Protests of U.S. policy in El Salvador are not surprising and are the result of a "well-orchestrated effort" by a "worldwide communist network," a senior administration official said yesterday.

Defending that policy before the House subcommittee on inter-American affairs, John A. Bushnell, acting assistant secretary of state for inter-American affairs, acknowledged that there have been protests in Latin America of the administration's decision to increase military assistance and dispatch 56 military advisers to aid the government of El Salvador.

"We know this is a top priority of the worldwide communist group," Bushnell said in explaining the protests. He said the State Department has evidence to support the contention that there is such a "well-orchestrated effort by communists" to stir up protests against U.S. policy but that he could not discuss most of the evidence at an open congressional hearing.

Bushnell and Lt. Gen. Ernest Graves, director of the Defense Security Assistance Agency, testified in support of the administration's request for $478 million in economic and military aid for Latin America during the fiscal year that begins Oct. 1.

Graves said the 56 military advisers, an increase of two from the initial estimate, are expected to complete their training duties in about six months. But he said it would be a mistake to assume that this would mark the end of the U.S. military presence in El Salvador, because there would be a continuing need for "follow-on training" in such areas as logistics and maintenance.

Questioned about the murders last December of four American missionaries in El Salvador, Bushnell differed with statements by Secretary of State Alexander M. Haig Jr. Haig said last week that investigators had developed a theory that the four women may have attempted or been thought to be attempting to run a government roadblock. Bushnell said he was aware of the theory but added, "I don't know of any facts or testimony that would support that theory or any other theory."

Bushnell was the senior State Department official who, at a recent briefing for reporters, complained that the press was paying too much attention to the El Salvador situation, a statement that brought a quick disavowal from the White House. Asked yesterday about the flap, Bushnell said his purpose had been to suggest that El Salvador was only one of a number of major foreign policy problems facing the country.

"I perhaps went too far" in making that suggestion, Bushnell said.