The First Minister was speaking at the University of Glasgow, where he delivered the Cardinal Winning Education Lecture.
The address, delivered during Catholic Education Week, signalled further support for faith-based diversification that could see the approval of Muslim schools in the near future.
"Scotland's diversity is a source of strength, not weakness," Salmond said. "For too long the attitude of some has been, at best, grudging acceptance of Catholic education and, at worst, outright hostility."
He added: "All faith-based schools play a significant role in helping to shape, inspire and strengthen our young people to learn. It's time to celebrate their contribution to Scottish education."
Salmond's support of Catholic education has again sparked debate over the success of faith schools and their future alongside the state system.
Catholic schools are proving increasingly popular with parents, regardless of their religion, because of the strong emphasis on community, the teaching of moral values and perceived higher levels of achievement.
Yet some claim the provisions in place to ensure the Catholic ethos in the 400-plus government-funded faith schools are divisive: the selection process for recruitment of some teaching staff involves approval by the local diocese.
Professor John Haldane, director at the Centre for Ethics, Philosophy and Public Affairs at St Andrews University, does not accept the idea that Catholic schools act as isolated educational islands.
He claims old sectarian divisions no longer hold in racially and culturally mixed environments. "A lot of Muslims are going to Catholic schools because there is more communality and moral teaching," he said.
"Nobody wants to make something of sectarianism any more. People are much less ideological, and much more concerned with choice."
Haldane cites research on Catholic schools in the US and England that suggests pupils achieve better results, but stressed this was not the most important factor in the schools' success. "What people seem to value about Catholic schools isn't exam results. It's more the strong sense of support, community, order and discipline they find."
Michael McGrath, director of the Catholic Education Service, said giving children the capacity to make principled judgements was the key to providing a well-rounded education.
"It's not to say young people in non-denominational schools don't acquire values, but the difference in the Catholic schools is we have a fairly explicit frame of reference for teaching these things," he said.
"Parents are choosing them because they are comfortable with the broad moral framework. In sex education, for example, lots of parents are quite happy we would be focusing much less on sex in a functional way, and much more on the idea of love in relationships."
Yet those wishing to separate religion and state education do not accept denominational schools are any more successful than mainstream counterparts.
Professor Eric Wilkinson, of the education department at Glasgow University, said: "There is no systematic modern evidence Catholic schools produce higher levels of attainment than non-denominational schools.
Despite backing from the Scottish government, Wilkinson believes Catholic schools must continue to make a case for future support. "There are lots of issues that need to be addressed. Preferential access for Catholics to certain teaching training institutions, for example. You could claim it's unfair the state supports just one kind of faith school."
He added: "Catholic schools can be potentially divisive in putting a wedge in fledgling friendship networks at a young age. They don't allow people to share their experience and understanding of the world."
Catholic school students across the country recently took time out to mark Catholic Education Week.
Jack Nellaney, headteacher at Trinity High School in Renfrew, said it was right to inform pupils about the purpose of Catholic schooling. "Faith is not something young people think about day in, day out, so it's important to give them a chance to reflect on faith in action."
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