The judge of Yajalon was surprised and infuriated when he found representatives of 55 Tzeltal Indian communities outside his office demanding the release of two long-time prisoners.

Not only was it unheard of that so many Indians should band together here, on the edge of Mexico's vast southern jungle, but even worse, they had been organized by Catholic priests and nuns.

"The clergy is stirring up the peasants," the judge complained to another notable of this tiny valley town. "It's time the army came to put some order in the place."

Last week, Yajalon's judge felt pressured enough to release one of the prisoners and, with influential churchmen from the whole region behind, the Indians, he backed away from calling outside help.

The incident illustrated both the growing participation of the Catholic church in Mexico's popular movements and the increasing tensions between church and state provoked by the militancy of progressive priests.

As Mexican bishops speak up more loudly against social injustice and priests become widely involved in political consciousness-raising in the the government has begun hitting back.

The offices of six Catholic organizations have been raided by police in the last eight months while numerous priest and lay workers have been placed under surveillance and have received telephone threats. Two priests have been killed under mysterious circumstances.

Church groups in the capital replied with angry advertisements in the press charging illegal arrests, confiscation of files, address books and office equipment. Conservative columnists and politicians in turn attacked the church groups as communists.

These confrontations are all the more surprising in Mexico, where the Catholic hierarchy has the reputation as the most cautious and conservative in Latin America.

While other church officials on this continent took a lead in protesting the grim conditions of the poor and the torture or killing of government opponents, the clergy in Mexico-one of the largest Catholic countries in the world-used to echo the government's own revolutionary rhetoric and preach passivity and submission.

The main explanation for this low profile of the last 30 years lies in Mexico's history of ferocious religious persecutions that destroyed the immense power and wealth of the hierarchy and drove the clergy out of their clerical garb, off the streets and even underground. The constitution adopted early in this century banned them from politics, and took away their rights to vote.

Those official terror campaigns - they began during the 19th century liberal reform and ended with notorious "Cristero wars" about 40 years ago - were launched because the church was on the side of the conservatives. Now it is criticized for turning radical and, once again, for meddling in politics.

One heavily political document, for example, was issued in December by nine bishops from the depressed and largely Indian south. It condemned government corruption, "the physical and psychological persecution, jailing, torture and even death," of peasants.

"Mexico is presently passing through one of the gravest crises of its history," the document said. "The political system is worsening the problems of the indigenous population and the peasantry . . . The current development model is leading us to intolerable levels of violence."

To the government's relief, such outspokenness is only found among a minority of the clergy. But church analysts say that minority is growing fast as the economic crisis aggravates the hardship of millions of Mexicans. Close to 40 percent of the work force is unemployed.

"The clergy is not simply reading Marxist literature," one key church source said, "but as the social crisis and repression grows, the local issues and dramas are radicalizing the priests. Five years ago, there were two progressive voices among the 62 bishops. Now there are 12, plus quite a few others who are quietly changing their mind."

The country's most controversial bishops are Sergio Mendez of Cuernavaca and Samuel Ruiz of San Cristobal, both of whom have become popular in their own diocese. They were appointed as conservatives but were radicalized by their experiences. From behind the musty, 16th century walls of his residence, Don Sergio supports union movements, strikes and student protests and mediates between groups of guerrillas, kidnapers and prisoners and the government. His spicy Sunday sermons are invariably reported by the press.

Mendez has survived his frequent conflicts with the conservative hierarchy by nourishing his own, very good relations with the Vatican. To keep his link with the government, he meets regularly with a Cabinet minister for a game of dominoes and political talk.

Samuel Rulz heads what is perhaps Mexico's most agitated diocese, where clashes between wealthy landlords and poor Indian communities have increasingly led to army intervention.

When Ruiz agreed to an interview in his San Cristobal home, he had just returned from a four-day trip on horseback to visit isolated jungle communities and the bishop seemed very discouraged. Mexico's economic development is taking place at a bitterly high social cost, he said.

"We say the church must support the poor and their organizations, but we're running very far behind events. Our so-called social peace is just a mask of deceit."

In the long run, Rutz, like other church leaders forsees inevitable conflict between church and state if the clergy's commitment to social reform grows. Despite past persecution, the church still has immense influence in Mexico and many Mexicans are deeply devout.

Mexico's centralized sovernment, which does not brook opposition easily, sees the 36,000 Catholic priests as the only nationwide organization outside its control.

The government, officially anti-clerical, is now seeking to improve its alliance with church conservatives rather than fighting the progressives and risking further bad publicity. This way a clash could not be kept within the church.

Church conservatives, by all accounts, have responded well. Last month, as an important preparatory document for the Latin American Bishop's conference - to be held here in October - was completed, cautious church priests made certain that copites were sent to the government, key bankers and the military.

Independent observes, however, say that Mexico's new, authoritarian primate, Archbishop Ernesto Corripio is rapidly losing prestige. He got off to a bad start by ordering a $10 entrance fee for the public to atteno his installation ceremonies, which were boycotted by indignant priests. He then alienated many progressive and moderate clerics by leading a public attack against Bishop Mendez, who had stressed Marxism a important in social reform. Such criticism should be voiced wihin the church, and not taken to the newspapers, the angry clerics charged.

Last week, Archbishop Corripio was admonished by Proceso, the country's most influential weekly. When a Proceso reporter tried to ask about his attack on Bishop Mendez, Corripio hastily took him by the arm and handed him over to another priest.

"This young man wants to confess, Father," said the archbishop and walked away.