ALEX Salmond's SNP government has been secretly working with the Catholic Church to defy new legislation on gay adoption.
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When that failed, Hyslop told the Church she was "comfortable" with plans by a Glasgow-based Catholic adoption service to refuse same-sex couples.
Gay rights campaigner Peter Tatchell accused Salmond of "conspiring with right-wing homophobic elements" in the Church.
The row follows the Scottish Parliament's decision in 2006 to allow gay couples to adopt children jointly.
On top of this, the Sexual Orientation Regulations (SOR) passed at Westminster meant that all bodies providing public services, including adoption, could not discriminate against gay people.
The regulations angered the Catholic Church, which unsuccessfully argued for an exemption for its adoption agencies, although religious organisations were given until January 1 this year to comply with the new law.
However, newly released correspondence shows how Hyslop tried to help the Church get round the equality legislation.
In a note of a meeting between Hyslop and Cardinal Keith O'Brien in July 2007, the education secretary's stance was spelled out: "The Scottish government position - as she had made clear in speaking to Whitehall - was that it would have been better for the exemption to end 2008 to have been made indefinite."
When the UK government refused to budge, Hyslop had further meetings with Church representatives about how to turn away same-sex couples.
Hyslop and the St Margaret's Children and Family Care Society, a Catholic adoption agency, met in October to discuss plans to reword the charity's constitution.
This rewording, which explicitly mentions the adoption agency's religious ethos, was aimed at allowing St Margaret's to provide its services solely to heterosexuals.
This loophole is contained in the SOR, which grants some leeway for religious groups to provide services to people of a "particular sexual orientation" only.
The note of the meeting stated: "It would then enable the Society to use the exemption under Reg. 18 of the SOR to provide services only to persons of a particular sexual orientation. If a same- sex couple applies to the Society, the couple would be directed to an appropriate agency. A service would not be provided by the Society to a same sex couple."
Hyslop made clear she was happy with the agency's approach at another meeting: "Cab Sec Hyslop emphasised that key issue is to help and support children and is comfortable with gay couples being referred on to adoption agencies that have more experience of working with gay couples."
Ronnie Convery, director of communications for the Roman Catholic Archdiocese of Glasgow, said: "It is not about evading the law, it's about using the law. Our understanding is that we will be able to continue to work within the law of the land, and work within the traditions of the St Margaret's agency."
Asked what would happen if a same-sex couple applied to the society, he said: "They would be treated with respect, but it would be explained to them that because of the nature of St Margaret's, they would be referred to the council adoption agency."
Tim Hopkins of the Equality Network said: "We would be very disappointed if the Scottish government's position is that any publicly-funded public service should be allowed to discriminate against any part of the population."
Tatchell added: "It is hugely disappointing and disturbing to learn that the SNP government has been secretly working with the Catholic Church on this issue. The SNP is officially in favour of gay equality, yet it seems to be conspiring with right-wing homophobic elements in the Catholic church's hierarchy to perpetuate discrimination."
Glasgow MSP Patrick Harvie said: "I'll be tabling questions to the government this week on this matter. Any attempt to get around the law should be stopped."
A spokesman for Fiona Hyslop said: "The Scottish government has always said that Catholic adoption agencies should be able to operate within the teachings of the church. That is a matter of public record, and we have made this view known to UK ministers and the Church itself.
"We understand that St Margaret's have successfully applied to the Office of the Scottish Charities Regulator for a change in their constitution, and will therefore be referring same-sex couples to other adoption agencies for assessment. That is a decision for the agency and the regulator."