Santiago Archbishop Juan Francisco Fresno today called Chile's state of siege "a grave reverse for understanding and peace" and charged that the government of Gen. Augusto Pinochet had "sown confusion" about the Roman Catholic Church.

In one of the strongest clerical criticisms of the government in recent years, Fresno read and distributed a pastoral letter that said a government crackdown on the media and its political opposition had provoked "disquiet, fear and anguish" among Chileans. Measures against the church, he added, "darken and endanger the communion with the church" of those who adopt them.

Fresno ordered the eight-page letter to be read in all churches Sunday. In the last week, the government has banned from Chile a priest heading the church's human rights organization and has censored Fresno's last two public statements.

Church officials here described Fresno's response as the strongest declaration he has made since becoming archbishop last year. "I want to be prudent," Fresno wrote, "but I will not be cowardly."

Fresno said the government should take "effective steps" to facilitate "a consensus over the present and future of our country." "The more people and organizations that participate . . . and the more liberty we have to do it," he added, the better the "guarantee of peace."

Fresno's address came as the official news agency Orbe reported the first wave of bombings since Pinochet's declaration of a state of siege Nov. 6. Orbe said 16 bombs exploded in seven cities during a two-hour interval last night, injuring three persons in the mining center of Rancagua.

Human rights officials said security forces continued to arrest political and union activists and students and that more than 500 persons were now being held without charges in jails and barracks around the country. The government announced yesterday that it was sending 103 persons with criminal records to a camp in northern Chile, where 250 persons already are serving terms of internal exile.

Students at the University of Chile boycotted classes here yesterday and held rallies against the state of siege. Today, student leaders said they had called another strike to protest the arrest of at least 15 students by police.

The two censored earlier statements by Fresno, a conservative whose appointment was openly welcomed by the military government, briefly criticized the expulsion order against Spanish priest Ignacio Gutierrez and mass arrests in a Santiago shantytown. Today's letter represented his first major comment on the state of siege and accompanying government measures against the church.

The archbishop accused the government of "casting doubt on the pastoral authority of the bishops" and "impeding public communication of pastors with their faithful in a country where the majority of citizens are Catholic and have a right to know the thinking of their bishops."

Fresno said that he was "deeply worried about the climate of violence" in Chile and condemned all terrorist activities. He added, however, that the government's normal authority gave it "sufficient tools to fight against all the terrorist excesses and also control those that come from the very security forces."

"I fear, in turn, that the state of siege means a grave reverse for understanding among Chileans and for peace in the country," he said.

Fresno called on Chileans to observe a day of "fasting and prayer" next week and said all Catholics should use the day to discuss how to "construct peace in Chile on the basis of truth, love and justice." He said the church would not allow that "other people determine the rhythm of the life of our church and prevent us from carrying out our own plans and fundamental evangelical activities."

Church officials said the statement reflected Fresno's determination to defy the recent pressure from the government, even at the cost of escalating an already serious confrontation with military authorities. After several months of deteriorating relations, the latest conflict began last week when Interior Minister Sergio Onofre Jarpa cited a meeting of bishops with Chilean political exiles in Rome as evidence that government efforts at political liberalization had failed. Two days later, authorities announced that Gutierrez would not be allowed back in the country and prohibited media from reporting Fresno's protest.

Yesterday, authorities stepped up the apparent offensive by banning a church-sponsored seminar on the theme of "the road to democracy." Officials said the event, part of a series of "social weeks" sponsored by the church for the past nine years, violated restrictions on the right to assembly.

In addition to distributing the letter and calling for the day of prayer and fasting, church officials said, Fresno had decided to refuse to negotiate with the government over the banning of Gutierrez or to remove him from his post as head of the Vicariate of Solidarity, Chile's principal human rights organization.

Chile's Conference of Bishops has also called a special meeting for Thursday and may issue its own statement on the government measures. "The church's role is one of service to the people," said Enrique Palet, the secretary general of the Vicariate of Solidarity. "We are going to use what strength we have to continue with our work at any cost."