Despite a recognition from most commentators that the final version of the strategy was largely a compromise document, both the Roman Catholic Church and Church of Scotland have outlined concerns about its implementation.
Michael McGrath, director of the Scottish Catholic Education Service, said he would be urging the Executive to produce materials advocating genuine abstinence - which he said the Catholic Church would offer to help design.
Mr McGrath welcomed the removal from the draft strategy of the "healthy respect" model of sex education materials, and described the introduction of "abstinence-plus", as the Executive describes it in the strategy, as a "positive move".
However, he said that the Church wanted to see materials beyond the "safe sex" model, which would advocate the positive value of abstinence so that pupils got other messages as well as ones on contraception and the avoidance of sexual diseases.
"Currently the sex education materials present no information or scant information on the positive aspects of abstinence - and we want to encourage the Executive to encourage that. We have offered to work in partnership with them on that," Mr McGrath said.
He condemned media speculation that the Executive had been under pressure to offer Catholic schools an opt-out as "alarmist".
Programmes of "relationships and moral education" in Catholic schools provided "positive, prudent and comprehensive information on aspects of sexual health, including contraception and the dangers of sexual infection, at appropriate stages, as numerous HMI reports can attest", he said.
"In contrast with other approaches which assume that all young people are sexually active and need to be instructed in the mechanics of 'safe sex', this approach positively encourages abstinence and develops skills for moral decision-making," Mr McGrath added.
In a swipe at Mike Rumbles, Liberal Democrats health spokesman, who has been outspoken over the Catholic Church's position regarding sex education, Mr McGrath described some critics of the Church's stance as "illiberal".
He welcomed the fact that the strategy did not lay down a single model of sex and relationships education, as the draft strategy had suggested.
"There has been some strange posturing going on. It is a pretty illiberal tendency to foist a moral viewpoint on the rest of the society, which is the thing we are usually accused of."
Meanwhile, the Kirk has met Peter Peacock, Education Minister, to share its concerns on training teachers in how to deliver sex and relationship education and working with parents.
Susan Leslie, secretary of the Church of Scotland's education committee, said: "HMI said recently that teachers still have not received enough CPD (continuing professional development) in this area. The minister agreed with us that CPD would still have to be a priority and we hope that some funding would be made available and put towards this.
"In terms of working with parents, while some schools and authorities have moved forward, the position is still patchy across the country. We really have to keep each generation of parents informed about what is in the programme, how it is delivered and how they can raise their concerns."
Ms Leslie said the Church of Scotland's departments would be meeting to develop a view on the whole sexual health strategy, but the education department was "generally content" with the Executive's policy.