The nation's Roman Catholic bishops yesterday urged all countries, but the United States in particular, to stop supplying arms to El Salvador and concentrate instead on promoting a political solution to the conflict there.

The bishops' statement on Central America called for U.S. economic assistance, "monitored . . . in terms of human rights criteria," for Guatemala and Nicaragua as well as El Salvador. The churchmen also urged a moratorium on the deportation of Salvadoran exiles in this country "as long as the present state of violence and turmoil exists in El Salvador."

In other action on the final day of their annual meeting here, the Catholic leaders also adopted a controversial pastoral letter on "Health and Healing" which for the first time asserts the rights of workers in the more than 600 Catholic hospitals throughout the nation to organize to bargain collectively and, in certain circumstances, to strike.

The pastoral letter also supports a "just and humane national health policy" that would assure "the right of all people to adequate health care."

The bishops' Central America statement, which was opposed by a handful of bishops who sought to delay or at least water it down, continues to place the church at odds with Reagan administration foreign policy in that part of the world.

As growing numbers of Catholic priests, nuns and lay persons -- and an archbishop -- have become victims of political violence in Central America in the last few years, Catholic leaders here have grown increasingly concerned about conditions there, taking their political cues from Central American bishops. The concern is heightened by missionary ties between the the United States and Central America, which give churchmen here a personal link to conditions there.

Those personal ties neutralized the kind of appeal voiced yesterday by Bishop John J. O'Connor of New York, who pleaded for delay of the statement and further study of the Central American scene. "When we make a statement recommending specific political actions, we must be precisely careful that we know what it is that we want done," he said.

Auxiliary Bishop John McCarthy of Galveston-Houston spoke of a fact-finding mission he had undertaken in El Salvador a year ago, and said four of the 20 persons he had interviewed were murdered within months of his visit. "This is not a political document," he said of the statement. "We are not concerned with who is president of El Salvador . We are concerned that whoever is president does not slaughter and murder their people."

By adopting the statement, McCarthy went on, "we are saying to the church in Latin America: 'We have been watching for 10 years . . . Now we are not going to sit it out any longer. Whatever influence we have in the North American continent, we are going to use that.' "

Only half a dozen of the 250 bishops present rose to oppose the statement in the standing vote.

The national umbrella organizations of religious orders of priests, brothers and nuns, who provide most of the missionaries serving in Central America, issued a statement offering "strong support" for the stand taken by the bishops.

The pastoral letter on health care also was overwhelmingly approved, despite efforts during debate to knock out the section on collective bargaining, which the powerful Catholic Hospital Association has opposed. Pope John Paul's recent encyclical on work, which gives strong support to labor unions, cut the ground out from under the CHA's objections.

One section of the health pastoral stresses the bishops' responsibility to set an example with "lifestyles which enhance our health and well-being" and rejecting "personal habits which can threaten our health such as smoking, excessive consumption of food and drink, abusive use of alcohol and drugs and neglect of proper exercise."