A Madrid military tribunal has seized copies of a controversail Spanish film, due to be screened at the Berlin Film Festival later this month, on the ground that the movie's scenes of tortures carried out by members of the paramilitary Civil Guard could constitute an offense against the armed forces.

The unexpected move indicates the growing ascendancy of the armed force in civilian affairs. It is also the first instance of censorship of an entire film since the 1978 constitution guaranteed freedom of expression.

The film, entitled "The Crime of Cuenca," is the reconstruction of a celebrated miscarriage of justice that occurred in 1913 when two peasants were tortured into confessing to a muder that had never taken place.

The decision by the military tribunal illustrates extreme sensitivity within the armed forces over the torture issue, following widespread allegations by suspected Basque terrorist and common criminals alike that torture is still practiced despite constitutional guarantees safeguarding the rights of prisoners.

Helen Matas -- an executive of the production company, Incine Films -- said she was "extremely surprised" by the military tribunal's move. She said she had been assured by the Ministry of Culutre, the government agency responsible for issuing exhibition permits, that "The Crime of Cuenca" would get the green light.

The ministerial assurance had come as time ran out for granting a permit. In Spain, the Ministry of Culture has two months in which to decide on a film's rating. Matas said that the film had been given a "S" certificate that would have banned it for anyone under 18, because of the violence in the torture sequences.

The military move had come as a surprise, Matas said, because "I believe that, with the constitution, there was no censorship in Spain. But I understand that at the present moment, to portray the Civil Guard as torturers is a delicate subject."

"The Crime of Cuenca" is filmed as a documentary reconstructing the allegations of a woman in the tiny, primitive village of Osa de la Vega that her son had been murdered by two local men, both shepherds with a reputation for troublemaking. The case is taken up by a cynical rightist politican and an ambitious district judge. The two shepherds are arrested and turned over the the Civil Guards, who are given instructions force a confession.

The torture scenes that follow are harrowing, but totally based on fact, according to director Pilar Miro. "We cut out some of the worst scenes, and we could have filmed even more gruesome stuff. It all happened. It's all documented," said Miro, Spain's leading woman film director.

A succession of bestialities, carried out on the instructions of a leering Civil Guard sergeant, elicit the necessary confessions, and the two men are imprisoned for long terms. Only after their release, in 1926, does the man they supposedly murdered, a local villager, reappear. The corpse that never was has changed villages, and was hiding from his mother in a hamlet a few miles away.

"The Crime of Cuenca" was selected by the jury of the Berlin Film Festival, and a copy with German substitles is already in Berlin awaiting the screening, scheduled for Feb. 25. The production company has over the past month given private screenings in Madrid and Barcelona to selected groups of politicians, lawyers, journalists and members of the armed forces.