A prominent federal judge, renouncing both his job and military government allegiance with a flurry of provocative court opinions and public statements, has underlined a growing number of conflicts between Argentina's civilian authorities and military leaders.

Judge Pedro Carlos Narvaiz, appointed to the powerful federal criminal court in 1979 as a loyal supporter of military rule, stunned both his colleagues and the government late last month by confronting the Army high command in one human rights case, then declaring Argentina's eight-year-old state of siege unconstitutional in another.

Narvaiz later resigned and left the country for Rio de Janeiro. There, in a series of beachside interviews with a popular Argentine magazine, he has charged the military with repeatedly manipulating and obstructing the nominally independent judicial system. He also said he had been threatened by government-allied paramilitary squads that he said "work with a certain degree of impunity."

"We must admit all of this has been something of a historic heap of refuse," Narvaiz said of military rule in one of the interviews this month. "And now is the time to clean it up, to drag it out in full view of the public, but without any fears."

The former judge's charges have been denied and branded opportunistic by government officials and by embarrassed sitting judges, who have long maintained that Argentina's judiciary is independent of the authoritarian military government.

But Narvaiz has not been alone in defying the armed forces' authority or revealing threats and harassment from suspected military agents. This week another Buenos Aires judge overturned a government ban on an issue of a popular magazine that covered Narvaiz's case. In addition, a high court official has alleged he was also harassed and threatened by paramilitaries who he said tried to break into his home and kidnap one of his daughters.

The court rulings and accusations against the government--which during most of its rule was rarely confronted by the courts--have marked several shifts by judicial and other former civilian supporters away from the military as its political authority has declined in the last year.

Even as judges have reversed government restrictions against the press and forced large releases of political prisoners, prominent news publications and commentators have shifted from support to harsh criticism of the armed forces. The Argentine Catholic Church, largely silent during years of military repression, has begun calling for a return to legal norms and has sought to arrange a resolution of outstanding human rights cases.

Many civilian leaders have been disillusioned by the military's actions during the Falkland Islands conflict with Britain and poor economic management, while others appear to be adjusting their positions in anticipation of a democratic government following the military's promised withdrawal from power in early 1984.

"Many judges feel pressured by the circumstances, the retirement of a military government and the imminent civilian government," said Judge Eduardo Francisco Marquardt, another member of the federal criminal court. "And many times they are ruling in a very different way than they did before, basically for political reasons."

The government's response has reflected its own divisions as its power has deteriorated. President Reynaldo Bignone and other government leaders, who have eased restrictions on the press and political parties and promised elections by November, have accepted the reversals and criticisms publicly as a natural development of the government transition.

At the same time, government authorities have frequently moved in recent months to tighten controls on the press and block court proceedings against military officials. Meanwhile, harassment and violence by paramilitary irregulars, often identified with the armed forces, have increased, leading many Argentines to expect both greater freedoms and what a magazine recently headlined as "the return of fear."

So far, opposition leaders point out, the armed forces have lost relatively little ground in the media or the courts. Despite the actions of judges like Narvaiz, human rights leaders point out that the courts have yet to take action in most cases of alleged human rights violations, including the estimated 6,000 to 15,000 persons who disappeared in the first years of military rule.

This week, a leading human rights group that specializes in legal action, the Center for Legal and Social Studies, charged that judges were actively obstructing investigations of hundreds of unmarked graves recently discovered in Argentina, despite evidence connecting the sites to military operations and the missing.

The military's relative influence over the judiciary and other civilian institutions is likely to be a key factor in Argentina's return to democracy and the resolution of military abuses, these rights leaders say. In recent months military and government spokesmen have frequently said that all alleged improper activities by the armed forces should be handled by the courts, and many officers privately add that they expect no major results from such investigations.

Since taking power in 1976, the military has depended on the court system to legitimize its rule and harsh tactics. Government officials have always maintained that the judiciary remains independent of the armed forces.

While seeking to maintain this image, the military also has installed its supporters throughout the top levels of the courts and in many local jurisdictions, and decreed several new laws that have limited personal rights and the strength of the courts.

For the first several years of military rule the Argentine Supreme Court rarely ruled against the government in an important case. When it did, such as in a 1979 decision ordering the release of imprisoned journalist Jacobo Timerman, military leaders tended to comply only on their own terms. Timerman was stripped of his property and citizenship and deported to Israel after the court decision.

Many human rights lawyers date the beginning of the judges' move away from military influence with the Timerman case. Since then the Supreme Court has consistently ordered the release of prisoners held for years without charges, and the government has responded with large releases of such prisoners in anticipation of court decisions.

Narvaiz's own career indicates the radical shifts of some judges below the Supreme Court level. Once a supporter of the military campaign against guerrillas and other opponents, Narvaiz responded to a large court action for the release of 300 political prisoners in 1981 by throwing the action out of court, then censuring the human rights lawyers who filed it.

In the following year, however, the judge's rulings underwent a dramatic change. By his own account, Narvaiz granted every petition that was brought to him seeking the release of political prisoners, and this year he began taking on investigations of military corruption and human rights violations.

In his final actions last month, Narvaiz challenged the Supreme Court to force Army Commander Gen. Cristino Nicolaides to release information connected to a politically motivated disappearance. He then used another human rights case to declare Argentina's state of siege unconstitutional. That judgment, which would effectively force the military to release all remaining prisoners held without charges, is widely expected to be overturned on appeal.

From his self-imposed exile in Rio de Janeiro, Narvaiz has accounted for his shift in position by saying he grew tired of being continually blocked in cases by military and government officials who he said denied him evidence or gave him false information.