The National Council of Churches governing board has attacked the grand jury system as riddled with abuses and urged its 31 member denominations to resist efforts by governmental investigators to obtain confidential information from church files.

The unanimous action by the 150 delegates to the semi-annual meeting of the board in Cincinatti, completed yesterday, stemmed from a grand jury probe into purported links between a military Puerto Rican independence group and a controversial Hispanic social activist organization funded by the Episcopal church.

The federal investigation of bombings believed to be the work of the military FALN has led to the imprisonment on contempt charges of two women lay ministers of the Episcopal church's National Commission on Hispanic Affairs. They went to jail rather than testify before the grand jury. They have denied knowledge of the FALN or its members but said their resistance was "on principle."

That principle was explained in the National Council of Churches resolutions as "the relationship of confidence and trust which is essential to the functioning of the religious community" and the "freedom of association and exercise of advocacy by (church) members and staff in their ministries and relationships with social action agencies and oppressed and alienated groups."

The grand jury issue is generating growing concern among church officials because of the dilemma faced by the Episcopal hierarchy.

In January Presiding Bishop John M. Allin voluntarily allowed the FBI into the Episcopal Church Center's office in New York for a week to look at non-confidential Hispanic commission files. He took this action after a subpoena served first on Bishop Milton Wood, church executive for administration, was withdrawn.

Officials of other churchs have conceded they are uninformed on the implications that similar actions against their files would raise about religious liberty and separation of church and state.

In one resolution passed without dissent the governing board expressed "deep concern" over the jailing of the women "as a matter of great significance to all member churches of the National Council." It directed council president William P. Thompson to appoint a commission to meet with Bishop Allin and "aid him in securing the early release of the two women, to restore their salaries and to pay their legal expenses."

In a resolution on grand juries, pending development of a more thorough policy statement, the council declared that "the use of the grand jury's powers to harass and pursue political dissidents is a departure from its proper constitutional function (to protect citizens from unwarranted prosecutions) and is a great threat to public order, lawful government and true domestic security."

The statement listed a binding procedure for council agencies and urged member churches, which have about 40 million members, to adopt the same course of action.

The resolution urged that churches not divulge the names of contributors, members, constituents, or any persons or groups with whom they have been working in a trust relationship, personnel files, correspondence, internal documents, travel or expense records without legal counsel and consent of the individuals involved.

Churches, the resolution said, should "give moral and material support" (including continuing salaries) to employees and members who "for reasons of principle refuse to testify before a grand jury and risk jail rather than expose others to harassment."

Churches which adopt all these and other recommendations "should be aware that they, or their members, may be faced with the risk of civil penalties, including citations for contempt of court, in their effort to establish judicial recognition of the church's right not to breach" confidential relationships, the resolution said.