A number of Catholic cardinals and bishops attending a synod on the Catholic Family have said they are "perplexed" by this week’s conciliatory discussion document on breaches of church doctrine.

They said this weekend's final document must not imply that the church approves "of their orientation and way of life" of gays and lesbians.

An official Vatican communiqué said that various synod discussion groups were also perplexed by the impression Monday's document may have created that the church is willing to legitimise what it calls "irregular family situations".

The document said homosexuals had "gifts and qualities to offer" and asked if Catholicism could accept gays and recognise positive aspects of same-sex couples.

In a dramatic change in tone from past condemnatory language, it said the Church should challenge itself to find "a fraternal space" for homosexuals without compromising Catholic doctrine on family and matrimony.

The Vatican stressed on Tuesday that the paper was still a "work in progress" and a definitive version would be issued after the meeting of 200 bishops ends on Sunday.

Cardinal Raymond Burke, from the United States, accused liberals in the committee that prepared the text of having railroaded the assembly.

He said it did not reflect a consensus position and demanded changes.

"While the document purports to report only the discussion which took place among the synod fathers, it, in fact, advances positions which many synod fathers do not accept," he told The Catholic World Report.

"A great number of the synod fathers found it objectionable," he said, asking Pope Francis to issue a clear statement defending marriage and the traditional family.

While Catholic gay rights groups around the world hailed the paper as a breakthrough, conservatives condemned it as a betrayal of church teaching and said its language had sowed confusion among the faithful.

"It (the document) is not what we are saying at all," Cardinal Wilfrid Fox Napier of South Africa told a news conference at the Vatican. "It is not a true message."

"The message has gone out that this is what the synod is saying, that this is what the Catholic Church is saying ... Whatever we say hereafter will seem like we're doing damage control," Cardinal Napier said.

One source in the synod said a number of other conservative bishops were "disappointed" by the document, known by its Latin name "relatio".

It was written by a committee of bishops after a week of speeches in the closed-door assembly. Participants have now broken down into ten small discussion groups to submit changes.

The final version will serve for further reflection among Catholics around the world over the next 12 months and as the cornerstone of a second and final synod on the family next year.

Cardinal Reinhard Marx of Germany disagreed with the conservatives, calling the document "an honest representation of how the debate developed".