Aimed at raising awareness on potential sexual issues and problems, the pilot "sex-ed" programme started last year and will continue to June 2014. Content is adjusted to the age of the pupils, who range from nine to 18 years old.
Introduced as a part of a wider obligatory health education programme in state primary and high schools, sex-ed covers topics such as sexually transmitted diseases, masturbation or gender equality, and aims to help avoid unwanted teenage pregnancy.
Vinko Filipovic, head of the government agency tasked with preparing the curriculum, told AFP that 2,000 teenage pregnancies were registered every year in Croatia.
Out of some 5,000 abortions every year, 400 are among adolescents, he warned.
"These alarming data showed a need to work on education of children as they mature sexually," Filipovic said.
No special textbooks are used for the programme, with topics discussed instead during class with mentor teachers or experts. Pupils receive just three hours of sex education every school year on average.
Despite such low-level school presence, the move has sparked the fury of bishops who, backed by pro-Church citizen groups, claimed that sex-ed would promote "pornography, promiscuity and homosexuality".
"Peace in our homeland is at stake," Zagreb archbishop Josip Bozanic said, slamming the curriculum change from the left-leaning government, in power since December 2011, as "destructive and dangerous".
One bishop, Valentin Pozaic, even called for overthrowing the "communist" government, comparing the authorities to Nazis.
"One should not forget that Nazis (also) came to power through democratic elections," Pozaic said.
Angry Church supporters have circulated anti-curriculum leaflets at the country's markets, shops and newstands.
"Don't you mind that your children learn about masturbation as a part of human sexuality?" read one leaflet urging parents to sign petitions against the curriculum.
GROZD, the national parenting NGO, claims the programme imposes a "view-of-life against values cherished by most parents".
-- 'Much about about nothing' --
The Church has a strong presence in Croatia where around 86 percent of the country's 4.2 million people are Roman Catholic.
But a survey of 1,300 people showed that 56 percent of those polled consider sexual education necessary. They were also against the Church's interference.
"What the Church is doing is a disaster," said 36-year-old Zagreb salesman Goran Miletic, a father of two.
"Children should be raised in reality and be prepared for everything they will face in life," he insisted.
But for Ivo Horvat, father of a teenager, the programme is "gay propaganda disguised in 'tolerance'".
Horvat is considering forbidding his 15-year-old son to attend the classes, a move the government has said will not be tolerated.
Many of the 516,000 pupils being given sex education seem to be the least upset with the debate.
"It is much ado about nothing," 15-year-old Laura told AFP, adding that the church "should not interfere in schools."
But Goran, 16, brushed off the need for sex-ed. "You can always ask older friends while teachers might feel embarrassed to discuss some issues with pupils," he said.
The government meanwhile has been quick to condemn attempts to shoot down its programme.
Education Minister Zeljko Jovanovic warned the Church was acting in an "unacceptable, ill-intentioned and defamatory way".
"Outside schools they can say whatever they want, but they can not decide what will be taught" there, he said.
Ivica Mastruko, a prominent sociologist of religion and former ambassador to the Vatican, said that the Church "cannot understand and accept that Croatia is a secular state".
As such, it "has the right to introduce all programmes in a way it believes appropriate", he said.
"This is yet another attempt and example (of) how the Catholic Church is trying to impose itself as a political force" in Croatia, Mastruko said.
After Croatia proclaimed independence in 1991, the Church -- firmly in the backseat in the post-World War II former Yugoslavia -- has become an increasingly vocal political partner of the authorities.
During the almost two-decades-long rule of late nationalist leader Franjo Tudjman and his HDZ party, agreements were signed with the Vatican guaranteeing budget funds for the Church and introducing religious teaching in public schools.
The Church has since repeatedly tried to impose itself as a supreme kingmaker in many secular issues in the country, which is set to join the European Union in July.
Under pressure from religious figures, Croatia's former conservative government adopted one of the most rigid laws in Europe on medically assisted reproduction, before it was amended by the current authorities in 2012.