Gen. Wojciech Jaruzelski was formally confirmed as premier by Poland's parliament today, and he immediately faced an intensified crisis with farmers threatening to strike and church leaders supporting their demand for a union.

Farmers in the southwestern city of Rzeszow, who have been occupying a government building to demand legal recognition of their union, greeted yesterday's compromise Supreme Court decision by vowing to continue their struggle even to the point of going on strike. The Roman Catholic bishops of Poland issued a statement supporting the farmers and criticizing the government's agricultural policy.

At the start of a three-day parliamentary session, it was announced that Gen. Jaruzelski will continue as defense minister, a post he has held for 13 years. Jaruzelski emphasized his military status by making the rare gesture of appearing in parliament in the uniform of a four-star general.

The military background of the new premier also was underlined by the Communist Party leader, Stanislaw Kania, who praised the 57-year-old general as "a patrotic soldier who has tasted battle." Two members of parliament abstained in the otherwise unanimous vote confirming Jaruzelski's appointment.

In his brief speech to parliament, Kania attempted to project for Jaruzelski the image of a determined soldier-politician committed to resolving the crisis through negotiation, but prepared to act firmly against "disorders." t This combination of rather contradictory qualities is apparently intended as the basis of the Communist authorities' new strategy for dealing with the independent unions.

At present, Poland appears to be enjoying a brief lull in its long-running industrial unrest, but a warning signal of the problems likely to confront Gen. Jaruzelski in the near future was provided by farmers' leaders raising the prospect of strikes unless the government recognizes a rural branch of the independent union Solidarity.

Yesterday the Supreme Court ruled that, as self-employed persons, private farmers could not form an independent union but might be allowed to set up associations. Associations enjoy less independence than unions in the eyes of the law and are therefore more susceptible to outside manipulation while having less influence.

The farmers in Rzeszow issued a statement saying, "We farmers are determined for anything." The statement added that the farmers did not want to strike but must be forced to do so. It called on parliament to change the law governing registration of trade unions.

In their statement, the bishops described "feeding the nation" as the basic problem confronting Poland. They condemned the "faculty agricultural policy pursued over the last few decades which has brought the nation to the verge of hunger."

The church statement said that, in addition to guarantees of land ownership, farmers "must have the right to freely associate, independently from existing associations." This it described as "natural justice."

It remains to be seen, of course, just how effective the Polish authorities' new policies will prove in practice. While it is true that traditionally Poles hold their Army in high esteem, the practical options open to Gen. Jaruzelski are just as limited and uninviting as those that confounded his predecessor, Jozef Pinkowski.

Political analysts believe that Jaruzelski's appointment has bought the authorities a little more time to repair their links with society while still retaining the confidence of the Soviet leadership. Jaruzelski's retention of the defense portfolio appears to reflect the need to have a man well-known to Moscow in this key position.

There were signs tonight that at least half a dozen government ministers will lose their jobs in a reshuffle expected at the end of the parliamentary session. The leadership held discussions with parliamentary commissions for agriculture, health, heavy industry, mining and education, indicating possible changes in these ministries.

In addition, two out of four deputy prime ministers are likely to be replaced. According to Polish sources, the new appointees could include the editor of the influential weekly Polityka, Mieczyslaw Rakowski, who is expected to become deputy prime minister with responsibility for information.

Meanwhile negotiations are reported to have broken down with students in the central city of Lodz. The students said they are prepared to drop a demand for the reduction of military service from two years to three months, but are insisting on extensive changes in the curriculum including the dropping of Marxism and Russian as compulsory subjects.

The student strike has spread to several other cities, including Poznan and Warsaw where the medical school has been occupied.

In his speech to parliament, Kania again criticized Pinkowski's government for failing to prevent the deterioration of economic and political problems following agreements with striking workers in August last year. Pinkowski himself, however, remains a member of the ruling Politburo and attended parliament today.

Kania said Gen. Jaruzelski had on several occasions insisted on the need for a political solution to the crisis.

"I am convinced he will be able to combine firm action against anarchy with pursuit of policies leading to socialist renewal," Kania added.