The ministers ask schools to teach with a certain tolerance and to speak with their pupils about sexual relationships and health by including same-sex relationships.
According to The Express, the Catholic Church issued a furious response, accusing the Government of showing it a "grudging tolerance" – and demanding guidance be rewritten.
Michael McGrath, director of the Scottish Catholic Education Service, said: "The SCES has encouraged the Scottish Government to move beyond the grudging tolerance which this draft and the original guidance showed towards the right of Catholic schools to follow Church guidance when teaching about sexual health and relationships, including marriage.
"We expect it, in its final guidance, to honour Nicola Sturgeon and Mike Russell's assurance it has 'no intention of requiring any denominational school to act contrary to the guidelines/policy established by the SCES or other religious authorities with a role in denominational education'."
A government spokesman reminded that all schools of the country could be subject to inspections in order to measure the quality of their education.
This government recently refused the addition of an amendment to the marriage equality law which would have allowed a protection based on religious freedom. Same-sex marriage is not legalized yet but was already approved by the Parliament in November 2013.
Scotland counts very large Catholic schools, it is thus a kind of revolution which is on the march.