About 2,000 Argentine troops arrived on a British ship at the southern town of Puerto Madryn from the Falkland Islands today amid heavy government security.

According to reports reaching here, the returning soldiers were disembarked from the British transport ship Norland while Argentine reporters and anxious families were kept at a distance by military authorities. Officials, apparently wishing to avoid public reports on the returning troops or their condition, followed a similar procedure when the British ship Canberra docked at Puerto Madryn Saturday with 4,172 Argentine soldiers.

The government's reluctance to allow publicity about the return of defeated troops reflected the disarray within the ruling armed forces, still deadlocked over selection of a new president. Air Force leaders threatened publicly today to withdraw their support from the military junta that is trying to find a replacement for Gen. Leopoldo Galtieri, who was forced out of his jobs as president and Army commander-in-chief last week.

Local news reports from the southern port cities of Trelew and Comodoro Rivadavia said a number of the returning troops were suffering from malnutrition or had hands and feet amputated because of gangrene and frostbite.

A common ailment was reported to be "trench foot," caused by the combination of freezing weather and the marshy ground on the islands. Soldiers' boots were frequently soaked through by moisture that caused infections, and the problem was aggravated by exposure to freezing temperatures.

Military officials here have given no official number of Argentine casualties in the conflict with Britain, but today reported that seven Argentine military police were killed at Stanley during the first week of June, without offering further explanation.

Argentine newspapers reported today that Argentine ships were believed to have arrived with returning troops at other points along the southern coast without any official announcement.

Foreign Ministry officials said they hoped to complete arrangements for returning the rest of the Argentine troops released by Britain within the next two days. Britain still holds about a thousand Argentine soldiers, including a number of officers, while awaiting Argentina's agreement to a formal end to hostilities.

The Air Force's threat to withdraw support from the government was communicated by officials to Argentine news services this afternoon after a morning meeting of the three-member junta failed to produce an agreement on a replacement for Galtieri.

Since Galtieri's ouster, the top commanders of the Argentine Army have insisted that he be replaced by another general, and have pressured for the resignation of the two other armed forces commanders and junta members responsible for Argentina's failed invasion of the Falkland Islands.

But Navy chief Jorge I. Anaya and Air Force commander Basilio Lami Dozo have been backed by their services in refusing to quit and have resisted the Army's move to install a retired general as president. Navy leaders said yesterday they favored naming a civilian president for the first time in six years, and the Air Force today appeared to have endorsed that position.

In the past several days of maneuvering over Argentina's new government, Lami Dozo has sought the presidential position for himself, but has been strongly opposed by Army leaders, who traditionally have held the balance of power in military political struggles here.

Today, an Air Force spokesman told the private news service Noticias Argentinas that "the Air Force has insisted, and for the last time, that they call a civilian for these duties."

Political sources and analysts expressed increasing concern about the power struggles within the military, which have been described as the most serious in Argentina since the early 1960s, when feuding military factions nearly led the country into civil war.

The only point of agreement reached by the three armed services a week after Argentina's surrender to Britain on the Falkland Islands, called the Malvinas Islands here, is that military rule will not extend beyond March 1984, when Galtieri's presidential term was due to expire, reports in Buenos Aires said.

An Argentine Army spokesman said later that the Army had agreed with the other services that the military should turn over power to civilians by 1984 and "give a concerted, institutional and democratic solution to the internal political situation of the country," United Press International reported.

With the government nearly paralyzed by the power struggles, Foreign Ministry officials said today that no further action had been planned in the conflict with Britain beyond Argentina's statement last week that it would not accept a formal end of hostilities in the South Atlantic until Britain withdrew its task force from the area.

The failure of the military to provide accounts of the fighting, the returning troops and the deliberations on the president provoked strong criticism today from some of the government's former civilian supporters.

Francisco Manrique, a prominent right-wing party leader, called for court trials for the principal military commanders responsible for the failed invasion of the Falklands.

"The country goes on without knowing the truth," Manrique said, "and the only truth is the pain, the shame of not understanding."