Unmarked helicopters carrying CIA employes routinely use airstrips recently constructed or improved by U.S. Army engineers in Honduras, and the flights apparently are for missions in support of Nicaraguan antigovernment guerrillas, military sources said this week.

The Reagan administration has said that the thousands of U.S. military personnel in Honduras since August for joint maneuvers are not assisting the CIA's covert support for the guerrillas of the Nicaraguan Democratic Force. But the CIA's use of the airstrips, as described by the sources, indicates that the intelligence agency and rebels have benefited from the military infrastructure installed during the maneuvers.

A desire by Honduran and Nicaraguan rebel officials to preserve the secrecy of these covert flights may have spawned conflicting accounts over the circumstances of the killing of U.S. Army helicopter pilot Jeffry Schwab on Jan. 11, according to U.S. sources familiar with the event.

The military sources said they assumed that the CIA flights were on behalf of the Honduras-based rebels, because the guerrillas are known to receive covert funding and other support from the intelligence agency.

They said the helicopters frequently carry Americans in civilian clothes bearing submachine guns or other arms.

The sources stressed, however, that Army engineers do not work with the CIA or directly assist the rebels, and they pointed out that the Honduran government has the right as owner of the airstrips to use them as it pleases.

"The nonmilitary aircraft land four or five times a week on the average. On a heavy day, there will be two or three stops for refueling," said one military source familiar with the flights carrying CIA employes. He said that the flights usually are in UH1H "Huey" helicopters.

The administration has said the joint military maneuvers here are necessary to build up the strength of the Honduran armed forces because of the perceived threat from the leftist Sandinista government in neighboring Nicaragua.

During the current maneuvers, called Big Pine II, the engineers have built a new dirt airstrip at San Lorenzo in the southwestern part of the country and have improved three others at Aguacate, Palmerola and Trujillo. Three rebel airmen captured by the Sandinistas and other rebel sources have named Aguacate as a major air base for the rebel front.

When asked about the reported CIA flights, U.S. military spokesman Col. James Strachan said that he had "no knowledge of that kind of activity" and added:

"We U.S. military forces on the maneuvers have no involvement of any kind with anticommunist Nicaraguan guerrillas. All facilities belong to the government of Honduras. Any other nonmilitary use of the facilities, if such use takes place, is a matter for the Honduran government."

The Honduran armed forces, which operate the airstrips, consistently have denied aiding the Nicaraguan rebels and have said that the guerrillas' struggle is an internal Nicaraguan matter. Honduran military spokesmen said yesterday that they would not be available for comment until Monday.

The precise circumstances of the killing of helicopter pilot Schwab remain uncertain because of conflicts between the official U.S. version and a series of accounts by Honduran officials and Nicaraguan rebel leaders. It appears possible, however, that much of the confusion was generated by fears that the incident would draw attention to the covert flights, several U.S. sources suggested.

According to these sources, the Hondurans and Nicaraguan rebels may have assumed that the Schwab flight was a covert one and made public a cover story that conflicted with the official U.S. version of the incident.

Nicaraguan forces shot down Schwab's helicopter and killed him after he made an emergency landing just inside Honduras. A dozen witnesses said the aircraft had overflown Nicaragua, although the U.S. government officially has acknowledged only that it was "possible" that the helicopter violated Nicaraguan airspace.

The U.S. government's account, first presented by embassy officials and later reaffirmed by an Army investigative team, said Schwab was on a routine flight ferrying two Army engineering officers from San Lorenzo to Aguacate. The aircraft strayed 25 to 30 miles off course to the southeast because of pilot error and heavy winds, bringing it close to the Nicaraguan border, according to the official U.S. account.

A differing account was presented in the week following the incident by seven officials, including a Honduran Cabinet minister, the Honduran Army colonel in charge of the region where the helicopter was downed, and the chief spokesman for the Nicaraguan Democratic Force. All said that Schwab's helicopter had flown to the border deliberately, and six of the seven said it had gone there to inspect a road under construction.

Such a trip would have violated self-imposed U.S. rules barring U.S. military aircraft from flying closer than five miles to the border. The embassy repeatedly denied that Schwab had planned to visit the border area.

Minister of Communications Carlos Handal and Nicaraguan Democratic Force spokesman Edgar Chamorro have publicly recanted their original versions of the incident. And Honduran and U.S. officials said that the other officials had done so as well. They acted under what one official called "heavy" pressure from the U.S. Embassy including a suggestion that future U.S. military maneuvers in Honduras would be jeopardized unless the matter was cleared up.

The Honduran government and armed forces went to great lengths at the end of last week to discredit the officials' accounts. The president's information office released a two-page statement saying that Handal "was not in possession of information" regarding the helicopter's flight route. And the armed forces' powerful chief, Gen. Gustavo Alvarez, publicly accused Army commander Col. Danilo Ferrera on having fabricated his account.

Both the government and Alvarez suggested that Handal and Ferrera had made up their stories to impress foreign correspondents who were interviewing them. The independent daily El Tiempo published a front-page cartoon Tuesday showing Handal and Ferrera with helicopters stuffed in their mouths.

While suspicions were raised by the effort to make the Honduran and Nicaraguan rebel accounts fit the embassy's, there were several indications that the road story could have been mistaken.

First, in contradiction with some of the original accounts, the U.S. government is not financing construction of the road, according to U.S. and Honduran officials and foreman Reynaldo Rodriguez in charge of construction of the road.

Second, Chamorro went out of his way to make public the account saying that the helicopter had gone to visit the road because he "was worried about what the Sandinistas would say about why the Americans were there," one rebel source said. Chamorro offered his account to at least three reporters in separate conversations in the two days following the incident.

Third, U.S. military personnel who knew Schwab and his passengers said they were confident the three were not involved in any kind of covert activity. The passengers, Capt. Christopher Maitin and Capt. Robert Green, were described by one acquaintence as "Mister Meek and Mister Mild."

Finally, military sources suggested that a radio message saying that a U.S. military helicopter planned to fly to the border town of Cifuentes on the day of the incident could have referred to a covert CIA flight and not to Schwab's as originally described. These sources said further that they suspected a U.S. Air Force radar facility had mistaken Schwab's helicopter for a covert flight and accidentally directed it toward the Nicaraguan border.

Col. Ferrera showed the radio message to two U.S. reporters Jan. 18 and said he was certain it referred to a Schwab flight. But U.S. officials insisted that no such messages are sent to Honduran authorities for flights such as Schwab's, and the military sources suggested that Ferrera was confused.

The Honduran government and Alvarez have said that Ferrera forged the message to impress his interviewers. Five Hondurans who know Ferrera dismissed this account as implausible, however, describing the colonel as honest and unimaginative.

Fererra has not been available for comment since he showed the reporters the message. A Honduran newspaper reported that he would lose his command for the alleged fabrication, but a Honduran military spokesman said the colonel's case was still under consideration by the Army High Command.