Is Spain sleepwalking into educational apartheid?

After 11 years of walking to her local school, Begoña Frutos decided to opt out of state education. Frustrated by her teachers' apathy and alarmed that her elder brother flunked his Bachillerato, the Spanish public exam for 18-year-olds, she badgered her parents into letting her move school. The daily commute to the classroom is now an 11km bus ride into the concrete jungle of Txurdinaga, a working-class suburb of northern Bilbao.

The 17-year-old chose Begoñazpi Ikastola, a private school run by the Catholic church but funded by the taxpayer. After a year, Frutos says she is much happier. "Yes I miss my friends but [state school] teachers did not care about the students. I am not religious but here the facilities are better. We use computers in the lessons, but it was just blackboard and chalk in my old school."

The student and aspiring lawyer is not alone in her enthusiasm. Spain's autonomous Basque region is education secretary Michael Gove's vision for schools made real: more than half of students here attend privately run but publicly funded schools known as concertadas, way above the Spanish national average of 26%. Basque students also score higher than British ones in international surveys.

Spain introduced concertadas in 1985. Like academies in Britain, concertadas are directly funded by the state, able to set teachers' wages and do not have to stick zealously to the national curriculum. They also select head teachers and pay them higher salaries – a radical departure from Spanish state schools where heads are elected by their peers and receive no extra cash despite onerous responsibilities.

Even critics concede concertadas represent value for money. Basque concertadas receive roughly half the 8,000 euros spent per pupil every year in state schools. Concertadas can raise extra cash by charging parents top-up fees.

Although the privately run schools are meant to be open to all, the combination of charges and a distinctive educational philosophy mean that they are effectively selective.

In the case of Begoñazpi, says head teacher Nerea Begoña, school is about "the doctrine of Jesus". Lessons begin with a daily prayer – and the school charges €1,000 a year to cover for books and five hours' extra lessons a week.

About a third of the 1,400 students travel more than 30km to attend the school. Classes are also almost exclusively white – with only "two or three" children from immigrant families attending the school. Unions say nearby state schools would have classrooms where a quarter of pupils are immigrants.

Fernando Aramendia, president of the school's parents association, says this "exclusivity" is to do with cost and religion. He says many immigrants, especially those from Latin America, cannot afford the extra cash. "It is also because we are Catholic. We cannot have Muslims here. It would be a contradiction. In public schools it is hard to find a white face now."

Experts say Spain is sleepwalking into a form of educational apartheid. "This a solid reality denounced recently by the Council of Europe," says Rafael Feito, an educational sociologist at Madrid's Universidad Autónoma.

The academic points out in a report earlier this year the council's human rights division chided Spain for creating "ghettos of immigrants or Roma children in some parts of the country … discriminatory practices in the admission process, allow [concertada] schools to select the students."

Feito says recent studies show that choice in education leads to segregation. "Parents want their children to meet pupils like them. It is a question of social status, of avoiding lower classes."

However schools dispute this saying parents are attracted by better results. In the Basque country 92% of 16-year-old pupils in concertadas obtain a high-school diploma, a few percentage points higher than public-school students.

However the real reason many say the government backs the concertadas is they save taxpayers money – which trade unions argue can be achieved only by increasing class sizes. Eduardo Fernandez Bodegas, the lead negotiator in the Basque region for 13 co-operative concertadas, denies the charge: "Public schools just spend too much money," he says.

This efficiency has not made concertadas immune from the effects of the financial crisis – and many are facing financial ruin after the government slashed public subsidies in 2008.

Bodegas says teachers at the concertada he runs in Bilbao have had to take pay cuts of €1,000 over the last two years. "The government said all public sector bodies would have to take a 5% cut in funding. So we had to cut [teachers'] wages."

Those who teach in privately managed schools say that bureaucracy – not parents – is the big issue. Aitziber Goikuria, who teaches geography at a concertada run by the Catholic Marist seminary in Bilbao, says that after qualifying she would have had to work "two or three years" as a supply teacher to get a permanent position in a government school.

"I did not want to be going from school to school just while I wait for a permanent job. So when I was offered a job (in a concertada) I took it."

The lessons from Spain are that unions have had to give half-hearted backing to the concertadas – as their members liked working in them. Many teachers prefer better-run, less chaotic schools with more freedom over how to teach.

However the changing face of Basque society means concertadas might inadvertently end up excluding talented immigrants. Just down from Begoñazpi school the graffiti scrawl extols the virtues of Athletic Bilbao, which famously selects team members only of Basque origin. Last year the club inveiled its first mixed-race player, Jonas Ramalho. His mother was Basque.