A private humanitarian organization called the Americares Foundation, working with the Order of the Knights of Malta, has channeled more than $14 million in donated medical aid to El Salvador, Honduras and Guatemala over the last two years.

The bulk of the supplies, worth about $10 million, has gone to hospitals and clinics in El Salvador, according to Americares' founder and president, Robert C. Macauley. But part of $680,000 in aid to Honduras went to Miskito Indians linked to U.S.-backed rebels fighting the leftist government of Nicaragua, according to a Knights of Malta official in Honduras.

Much of the $3.4 million in Americares' medical aid to Guatemala has been distributed through the armed forces as part of its resettlement program of "model villages" aimed at defeating leftist insurgents, said the official, Guatemalan businessman Roberto Alejos.

Prominent in the U.S. end of the operation are businessman J. Peter Grace, head of the W.R. Grace conglomerate and chairman of the American division of the Knights of Malta; attorney Prescott Bush Jr., brother of Vice President Bush; former treasury secretary William E. Simon, and Macauley, a New Canaan, Conn., businessman.

Among the 1,750 U.S. members of the Knights are CIA Director William J. Casey, former secretary of state Alexander M. Haig Jr. and former secretary of health, education and welfare Joseph A. Califano, although they apparently are not involved in the Americares effort. Former national security affairs adviser Zbigniew Brzezinski is honorary chairman of Americares' board of directors.

The Knights, formally called the "Sovereign Military Hospitaller Order of St. John, of Jerusalem, of Rhodes and of Malta," was founded in 1099 to aid the wounded and to battle Moslems during the Crusades. Based in Rome, the devoutly Roman Catholic order has 10,000 members in 42 nations and is recognized diplomatically as the world's only sovereign nation without territory. It has ambassadors in 40 countries. Medical aid thus can be moved through diplomatic "pouches" into needy countries without going through customs, Grace said in an interview.

The Americares program is among the largest of dozens of private relief efforts in Central America. Under the Reagan administration, the U.S. Agency for International Development is trying to encourage private involvement in foreign aid worldwide, partly to bypass bureaucratic tangles in the receiving nation and partly to avoid the strings that Congress often ties to federal programs.

Alejos, co-chairman of the Knights of Malta in Honduras, said in a recent interview with freelance reporter Peter H. Stone that "some of the Americares aid went to the Miskito Indians" there. Congress has banned U.S. aid to Nicaraguan rebels, called "contras" and based in Honduras. The Miskitos are divided, but several tribes have joined the rebels.

Alejos said eight Honduran hospitals have benefited, including one in the Indian area called Mosquitia.

In Guatemala, Alejos told Stone, the Guatemalan army delivers Americares medicine to people in the model villages, which are along the Mexican border.

Alejos, a major sugar and coffee grower, lent his Guatemalan estates to the Central Intelligence Agency in 1960 to train Cubans for the Bay of Pigs invasion.

But all officials contacted insisted that neither the Knights nor Americares has any political involvement in Central America. Both groups have extensive histories of charitable work, particularly with refugees in Pakistan, Afghanistan and Poland.

Grace said he started the medical shipments to Central America in 1983 by calling Macauley and suggesting that Americares and the Knights of Malta work together there. Bush and Simon, members of the Americares advisory committee, help to raise funds and obtain free medicine.

Grace, Bush and Macauley said there is no link between their effort and Reagan administration policy in the region.

Instead, they said, they "beg" free or nearly free medicines and equipment donations from major U.S. companies and wangle cut-rate shipping to Central America. The aid then is distributed to civilian hospitals, clinics and medical centers by local Knights of Malta members, who generally are well-to-do businessmen, lawyers, doctors or others with such facilities as warehouses, trucks or planes at their disposal.

Such people do not tend to be sympathetic to leftest guerrillas, and critics charge that medical and humanitarian aid helps the Salvadorans and the Guatemalan government fight the rebels by freeing other money to buy arms.

"On that basis you'd never be able to help anybody anywhere," Macauley said.

Medical companies whose officials have praised Americares as a low-overhead, efficient operation to which they donated medical supplies include the G.D. Searle & Co. of Skokie, Ill.; Sterling Drug Inc. of New York; Merck & Co. Inc. of Rahway, N.J., and Richardson Vicks Inc. of Westport, Conn.

Macauley said his foundation has received donations from the top 40 or 50 U.S. medical companies, which can deduct such contributions. He said that Americares has shipped $28 million in medical aid to trouble spots since incorporating in 1982 and that it has just one paid employe, a secretary/bookkeeper. All other labor is donated, he said, and funds are raised only to cover transportation, packing and shipping costs.

He said has received 10 percent of his funds from the Christian Broadcasting Network, mostly during the campaign to aid Afghan refugees.

"A $1 donation ships $20 worth of medicine," he said. "People like that."

Macauley is by all accounts the spark plug of the operation, "the best salesman I've ever known," Grace said. "Eighty percent of it is his work."

Asked why the Knights of Malta turned to Americares rather than to established aid groups, such as the Red Cross, Grace said, "The Knights have been doing this for 900 years. They have their own cross the Maltese cross . . . . They'd consider themselves way beyond the Red Cross."

Macauley, who is not a Knight of Malta, said another reason is Americares' speed and efficiency. "The Red Cross does wonderful work, but you go through committees and it takes them three to six months to move."

Americares, he said, precedes its shipments with volunteers who assess the country's needs and monitor the shipments -- with a television film crew, in El Salvador's case -- to make sure they are delivered to the needy.

Aid to Honduras and Guatemala is controlled by the Knights there, including Alejos. "We don't second-guess them; we have complete trust in them," Macauley said. "My feeling is that none of the aid goes to the 'contra' forces, but I couldn't say that absolutely none of it does."

Macauley said he had never shippped military equipment but would do so at the request of the U.S. government. "We've never been asked. We are a humanitarian group . . . but as a citizen it's incumbent on me to carry out the orders of the commander-in-chief."

Macauley also said he "wouldn't reject sending aid to the government of Nicaragua, but I wouldn't be able to control distribution . . . . The Knights aren't active there."

Heading the Knights of Malta in El Salvador are Gerald Coughlan, a retired Federal Bureau of Investigation agent and executive of International Harvester Co., which warehouses Americares shipments before distribution, and Miguel Salaverria, manager of the Prieto S.A. coffee export company.

Salaverria said there are about 20 Salvadoran Knights but only five or six remain in the country. The United States Embassy "is very helpful" in arranging transport into El Salvador, while the Salvadoran armed forces help move the supplies, he said. Salaverria said none of it goes to military hospitals or to guerrilla strongholds.

"We are not helping either side that's fighting," he said.

However, at least one pro-government group, the Air Commando Association of Fort Walton Beach, Fla., claims to have used Knights of Malta warehouses in El Salvador. Retired general H.C. Aderholt, head of the 1,500-member group, told Stone that the commandos delivered food and medicine to the Knights' facilities and that together they "get good support from the Salvadoran air force commander."

Aderholt said the association has distributed to El Salvador $4.5 million in food and medicine provided by the Christian Broadcasting Network and World Medical Relief. He said liberals in Congress have tried to "tie to some sinister plan with the CIA," which he said is incorrect.

Yet, a panel that met at the Defense Department this month urged the United States to move away from conventional warfare tactics in El Salvador and to apply the lessons of counterinsurgency warfare, including increased civic action.