The comments by Michael McGrath, director of the Catholic Education Service, will be seen as a rebuke to Bishop Joe Devine who provoked a storm of protest when he was reported in the Sunday Herald as saying that hiring or promoting openly gay teachers was "incompatible with Catholic social teaching".
Bishop Devine, president of the Catholic Education Commission, was also quoted as saying that the Charter for Catholic Schools, launched in June, backed this view. Mr McGrath said that the charter has nothing to do with an individual's sexuality. Asked if he was relaxed about homosexuals teaching in Catholic schools, he replied: "Yes."
The charter, which has been issued to all 428 Catholic schools in Scotland, states simply: "All staff appointed to a Catholic school are expected to support and promote the aims, mission, values and ethos of the school, as illustrated in this charter." It also calls on Catholic schools to uphold the Church's moral teaching and to practise an "inclusive ethos".
The Catholic Catechism, a summary of the official teachings of the Church, states that homosexuals should be treated with "respect, compassion and sensitivity", and that "every sign of unjust discrimination in their regard should be avoided".
The catechism also says, however, that homosexual acts are not acceptable and that homosexuals should be "called to chastity".
One of Scotland's leading Catholic headteachers, George Haggarty of St John's High in Dundee, pointed out that the Church has always been clear that candidates for teaching posts in its schools must pass the test of their "religious belief and character".
"I cannot deny that someone's moral character is part of the approval process," Mr Haggarty said. "But the important thing is not to judge the person but to judge the contribution he or she can make to the Catholic school."
The "bottom line" for the Church was that pupils must be educated in line with the wishes of their parents, and there may be cases where an individual's lifestyle was at odds with this. "That is where the school would have to give voice to the views of the wider Catholic community," Mr Haggarty said.
Frances Gilpin, president of the Catholic Headteachers' Association of Scotland, said the charter was "not designed to exclude and it is unfortunate that it is being seen in that way".
Mrs Gilpin, head of Notre Dame High in Greenock, said any gay teacher considering a job in a Catholic school would have to decide whether they could support the aims of the charter, and a referee would have to confirm that. The candidate is then passed to the bishops for approval.
Meanwhile the education authorities, who were wrongly reported to be in negotiation over the charter, which is a Church document, issued a strong warning that they would step in if the hierarchy was seen to be discriminating against any group of staff.
"We would stop the process in its tracks," Colin Dalrymple, general secretary of the Association of Directors of Education in Scotland, told The TES Scotland. "It would be the authorities, as the teachers' employer, who would be challenged if there was any discrimination under employment law, and it is in our interests to ensure that none exists."