U.S. Attorney Joseph E. diGenova once again dismissed charges yesterday against five leaders of apartheid protests at the South African Embassy but took issue with those who have accused his office of having an erratic, contradictory policy toward the prosecution of demonstrators at other embassies.

"The charges were dropped for appropriate reasons which is our policy not to enunciate," said diGenova, denying any contradictions. "The issue is . . . not all embassies but specific embassies which are the subject of specific protest."

Since the South African Embassy protests began last November, diGenova has dropped charges against more than 2,300 demonstrators, saying the cases lacked "prosecutive merit." But prosecuters in his office, which in the meantime has prosecuted Soviet Embassy and abortion protesters, warned that the Justice Department would take a different view if the protests turned violent or if demonstrators were arrested a second time. DiGenova said, however, that was never official policy.

Charges were dismissed yesterday against D.C. Del. Walter E. Fauntroy, Randall Robinson and three other members of the Free South Africa Movement steering committee, who were arrested for the second time at the embassy last month. Each had been arrested at the embassy in the early days of the protests there, and their re-arrests, in effect, challenged diGenova to prosecute them.

"No self-respecting prosecutor would permit himself to look so inconsistent and so foolish," the five protesters said in a statement following the dismissal of the charges.

They accused the Reagan administration of deliberately dropping charges against the South African Embassy demonstrators in order to deny them the chance to air their antiapartheid arguments in a courtroom.

"This is an indication of the administration's own belief in the bankruptcy of its policy of constructive engagement," said Robinson, national coordinator of the apartheid protests. " . . . They clearly understand that it would be the administration on trial, not the five of us."

In addition to their two embassy arrests, Robinson and the others were arrested here in April for a sit-in at Deak-Perera, a firm that deals in foreign coins, including South African krugerrands. The company declined to prosecute.

DiGenova cited a recent D.C. Superior Court ruling that supported his decision to prosecute a demonstrator at the Soviet Embassy while dropping charges against the apartheid protesters. Nearly all the protesters have been charged with demonstrating within 500 feet of the embassy, a misdemeanor.

The judge turned aside allegations of selective prosecution in the case of the Soviet Embassy demonstrator, Vanno Om Strinko, saying U.S. relations from country to country vary significantly. A case of selective prosecution, the judge said, could apply if protesters arrested at the same embassy were treated differently.

Since the start of the South African Embassy protests Nov. 21, there have been conflicting statements about why the demonstrators are not being prosecuted.

After the first arrests, the U.S. attorney's office initially proceeded with prosecution, saying it had been unable to contact anyone at the State Department or the embassy. Later, diGenova said the cases lacked prosecutive merit, and sources in his office said they did not want to clog courtrooms with such cases. The U.S. attorney also said at the time that the decision to drop charges had been made "without any consultation from anybody in the White House, the State Department or the Justice Department."

DiGenova said yesterday he had consulted with the embassies in question and with the State Department about the antiapartheid cases but had not been "ordered" about how to proceed.

"It is regrettable that these individuals have sought to politicize the criminal justice decision-making process," he said.

A spokesman at the South African Embassy said it was "a good assumption" that the embassy was consulted about whether to prosecute the protesters. But he said the actual decision "is still up to the U.S. attorney."

The Haitian Embassy, where charges were recently dismissed against three protesters there, declined to comment on the dismissals. A prosecution source said, however, that since the demonstration occurred inside the embassy, embassy officials would have had to temporarily give up their diplomatic immunity to testify in the case.

A spokesman at the Embassy of India said it would like protesters to be dealt with "in accordance with the laws," while the press attache at the French Embassy said the embassy had never had protesters and had no policy for dealing with them.

Nikos Papakonstantinou, press attache at the Greek Embassy, called the 500-foot rule "a nuisance to police . . . people have a right to demonstrate." He said no Americans had demonstrated against his country "since the Greek junta. We take a very nonchalant attitude about protesters."