Catholic bishops have rejected a landmark welcome to gays, showing deep divisions at the end of a two-week meeting sought by Pope Francis to chart a more merciful approach to ministering to Catholic families.

The bishops failed on Saturday to approve the section on ministering to gays, originally titled "welcoming homosexuals", the content of which had already been watered down to accommodate objections.

A two-paragraph section of the final agreed document was titled "Pastoral attention towards persons with homosexual orientations". The previous, three-paragraph version had been called "Welcoming homosexuals".

The earlier version spoke of "accepting and valuing their sexual orientations" and giving gays "a welcoming home".

The final version eliminated those phrases and most of the other language that church progressives and gay rights groups had hailed as a breakthrough.

It repeated earlier church statements that gays "should be welcomed with respect and sensitivity" and that discrimination against gays was "to be avoided" and also stressed "there is no foundation whatsoever" to compare homosexual marriage to heterosexual marriage, calling heterosexual marriage "God's plan for matrimony and the family".

Conservatives had harshly criticised the draft on the basis of current church doctrine: that gay sex is "intrinsically disordered", but that gays themselves are to be respected, and that marriage is only between a man and woman.

Two paragraphs concerning the other issue at the synod - whether divorced and civilly remarried Catholics could receive communion - also failed to pass.

"We could see that there were different viewpoints,'' said Oswald Gracis, a cardinal from India, when asked about the most contentious sections of the report on homosexuals and divorced and remarried Catholics.

Walter Kasper, a German cardinal and the leader of the progressive camp, said he was "realistic'' about the outcome.

Francis insisted in the name of transparency that the full document be published with the voting tally.

The document is to serve as the basis for future debate leading up to another meeting of bishops next October.