Thousands of demonstrators marched through downtown and gathered in front of the presidential palace here today to denounce the military government's controversial effort to justify the thousands of missing persons from its war against internal opponents.

The demonstration, built around the weekly march by families of the estimated 6,000 to 15,000 persons known here as the disappeared, came after a week of heavy criticism of the armed forces by political parties, European governments and the Vatican. The criticism appears to have frustrated the government's effort to end debate about its human rights record.

The lengthy official report issued by the armed forces last week described their four-year campaign against terrorists and leftists as an act of military service exempt from civilian court investigations and declared that those missing were "considered judicially and administratively dead."

Most of the missing are believed to have been abducted by security forces between 1975 and 1979, tortured for information, then summarily killed.

The government of retired general Reynaldo Bignone recalled its ambassador to Italy yesterday after two strong condemnations of the report by Italian President Sandro Pertini, who said the government was trying to justify "horrible crimes against the Argentine people."

Italy, France, Spain and other European countries have several hundred citizens among the Argentine lists of disappeared, and their governments have long pressured the armed forces to provide a full accounting for them.

A U.S. State Department spokesman noted the internal dissatisfaction with the armed forces report last week, but the Reagan administration has so far refrained from directly criticizing the government's policy.

At today's demonstration, the group called Mothers of the Plaza de Mayo, who have marched in front of the presidential palace every Thursday for four years, demanded trials for those responsible for the disappearances and said in a statement that "we will continue demanding our children alive, and will never accept the aberration of 'administrative-judicial death.' "

"I am here because I am a mother and because I don't want this tragedy ever to be repeated for my young children," said Liliana Gentile, a 33-year-old woman whose cousin disappeared in 1977. "This is something we can never resign ourselves to accepting. It is a cause we can never forget."

The family members, dressed in now-traditional white head scarfs, were joined by passers-by and leftist political groups to form a crowd of more than 3,000 that stood facing the pink government palace and chanted "Murderers" and "Justice for the guilty."

Government officials, apparently eager to avoid further international criticism, made no attempt to disperse the protesters, and police uncharacteristically did not stop the crowd from marching down the wide avenue leading from the palace to the closed national congress.

In recent days, military officials have appeared surprised by the heavy criticism of their report seeking to justify the disappearances, prepared and debated within the armed forces for more than six months before being broadcast on national television last Thursday.

Military officials have now indicated that they will renew work on a formal amnesty law granting legal immunity to all those who participated in the official repression as well as some of the leftists in exile.

Armed forces leaders reportedly had hoped to avoid sanctioning such a law--with its implicit recognition that crimes were committed--by officially declaring their actions as military duty. After the sharp attacks on last week's justification, however, accounts leaked to the Argentine press yesterday said the law had been revived and would be decreed later this month.

Human rights leaders said their protests were the beginning of a campaign against the military's report and the prospective amnesty law that would culminate later this month in a mass demonstration coordinated with Argentina's major political parties.