American Catholic bishops are considering the establishment of a nationwide watchdog process that would help all religious groups guard against government interference in church affairs.

The proposal by Cardinal Terence Cooke of New York came at the conclusion of a special half-day session of the National Conference of Catholic Bishops devoted to a consideration of what the prelates termed "recent government incursions into church bodies."

The discussion, which began on a scholarly and historical level with the presentations of two experts in the field, quickly became emotional as the participants vented their frustrations over what they perceived as unfair treatment by government agencies.

Bishop after bishop took the floor to complain that government regulatory agencies, particularly those related to the Department of Labor, are treading on constitutional guarantees of religious freedom by seeking to regulate unduly church institutions, especially parochial schools.

"Acts of subversion are being perpetrated by some agencies," asserted Cardinal John Krol of Philadelphia.

He complained of "sometimes terrorist tactics of government agents who come in without an appointment, and want to see your files," and operate in a manner which "implies you are guilty until you prove yourself innocent."

Parochial school systems in Philadelphia have been embroiled with the National Labor Relations Board for several years over the right of lay teachers to organize. Other Catholic schools in Pennsylvania, as well as elsewhere, have tangled with the government over failure to make unemployment compensation payments for lay employes.

Krol did not specify what had precipitated the encounters he complained of.

THe issue of whether the NLRB has jurisdiction over parochial school employes is currently before the Supreme Court in a case involving schools in Chicago and Fort Wayne.

Catholic leaders feel they are being whipsawed by government on their schools. On the one hand, courts have repeatedly ruled the schools are religious institutions and therefore not eligible for tax aid. But on the other hand, regulatory agencies such as the NLRB treat them as secular or commercial enterprises in the enforcement of regulations.

The most heated outburst of the afternoon came from Bishop Joseph McNicholas of Springfield, III, who began by recounting the hierarchy's strong support of President Carter's efforts for the Panama Canal treaties - efforts, he said, that "made possible the passage" of the treaties.

"The same White House (that welcomed the bishops' help in winning approval of the treaties) appointed Secretary (Ray) marhsall" whose Labor Department regulations are troublesome to Catholic schools and other institutions, he said.

"The White House and the administration used us when it was something they wanted," McNicholas said. He suggested that somebody from the bishops' conference "ought to knock on the White House door and ask them, "What did Marshall mean? Why is he doing this to us?"

Cardinal Cooke proposed enlisting the aid of church colleges across the country in "an ongoing monitoring of the situation" on an ecumenical basis to develop an awareness of incursions by government into religious affairs. Conference leaders said later they expected some action on the Cooke proposal later in the week. The conference, the bishops' fall meeting, concludes Thursday.

Earlier, about 25 of the more than 2,000 women who had attended a weekend conference in Baltimore on opening the Catholic priesthood to women gathered to confront the bishop as they left their morning session at the Capital Hilton here.

A committee of bishops was designated to meet privately with the women. Russell Shaw, director of communications for the hierachy, who sat in on the session, told reporters later that the role of the bishops' committe was only to "listen and report."

He said "they listened this afternoon" but will not report their conversations to the full body of bishops until the hierarchy's spring meeting next May.

Only one - Bishop Charles A. Buswell of Pueblo, Colo - of the nation's more than 340 Catholic Bishops attended any of the sessions of the ordination.