Terry Prendergast, the chief executive of Marriage Care, claimed there is "no evidence" that children do better if they are brought up in a traditional two-parent family.
He claimed that those who live together out of wedlock are trying to lead good lives but find themselves "consigned to the dustbin" by the church.
His comments – to be made this weekend to Quest, a group of homosexual Catholics – go directly against the church's teaching, which holds that homosexuality is sinful and that families should be based on the marriage of a man and a woman.
Mr Prendergast said: "We see, for example, that statistically children do best in a family where the adult relationship is steady, stable and loving – you should note here perhaps that I stress adult, not married, since there is no evidence that suggests that children do best with heterosexual couples."
He claimed that God was present in the relationships of married, homosexual and cohabiting heterosexual relationships where there was "commitment, consent and covenant".
He went on: "They want to live good lives according to the precepts of the Gospels. They are an advert for the Church, an advert that the Church often ignores or consigns to the wastebin."
Mr Prendergast also said the Government cares more about families than the church, because it supports people who are unmarried and allows same-sex civil partnerships.
"The fact that there are all kinds of benefits available for different family forms, and legal imperatives to support families suggests that the State is even more concerned for families than Church."
Marriage Care, which provides relationship counselling, is partly funded by Catholic dioceses but a spokesman for the church in England and Wales rejected Mr Prendergast's arguments.
He told the Catholic Herald newspaper: "Defining 'family' is a notoriously difficult task. Yet the views expressed by Terry Prendergast about the definition of family and marriage are clearly not a reflection of the Church's teaching, nor those of the Bishops' Conference.
"Responding to the needs of children is also complex. The Church's vision is that the crucially important quality of stability in family life needs gender complementarity and role modelling too."
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