The Roman Catholic church is among those objecting to the new curriculum introduced in 2007 by the Socialist government of Prime Minister José Luis Rodríguez Zapatero.
Lessons on sexuality, human rights, the equality of men and women and the structure of political systems are taught at both primary and secondary level.
As well as the Church, the opppostion Partido Popular urged parents to boycott the lessons.
The party lost last year's election on a platform of overturning gay marriage and removing the right of gay couples to adopt.
Spain's Supreme Court has rejected the decision of an Andalusian court that a pupil could miss the class as a conscientious objector.
Conservative and Catholic activists have pledged to take the case to the European Court of Human Rights.
Mercedes Cabrera, the minister of education, said after the Supreme Court's ruling yesterday:
"The reality of today's Spain is that there are all sorts of types of family and we have laws that recognise all kinds of relationships.
"People say that the state wants to occupy the territory that the church used to occupy. That's absolutely untrue."
During last year's elections the Church was accused of interfering in the political process.
Spain's ambassador to the Vatican met with Church officials to protest.
Ambassador Francisco Vazquez expressed his "perplexity and surprise" at a statement issued by the Spanish Bishop's Conference.
"Catholics may support and join different parties it is also true that not all (electoral) programmes are equally compatible with the faith and Christian demands in life," the bishops said.
This was widely interpreted as an instruction to the faithful not to vote for parties that support gay marriage or negotiate with Basque terrorists.
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