At the end of 2010 Adam Fischer resigned from his position as director of the Hungarian State Opera.

He stood down not on artistic but on political grounds: an act of personal and public protest against new media laws being proposed by the Hungarian Prime Minister Viktor Orban.

The laws, which curtailed the independence of both press and cultural institutions, were implemented regardless on January 1, 2011, the same day that Hungary took up the rotating presidency of the European Union. Fischer travelled to Brussels along with other leading Hungarian artists to voice his concern to the international community. "The problems run far deeper," he told a gathering at La Monnaie opera house. "Even more worrying are the changes to the national constitution and the rise in anti-Semitism, homophobia and xenophobia in Hungarian society."

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As well as one of Europe's leading conductors, Fischer is one of classical music's most vocal advocates for cultural freedom and equality. Within his native Hungary he has taken a prominent stance against the right-wing regime of Orbán; internationally he runs a campaign website called Artists Against Racism. Next week Fischer works with the Scottish Chamber Orchestra for the first time, and though our interview was ostensibly set up to discuss the Haydn concerts he's conducting in Edinburgh and Glasgow, the conversation lingers first around his political activities.

I ask how the situation in Hungary has changed in the two years since that speech at La Monnaie. "It's still a very sad story," he tells me. "Actually I think that things are going in the wrong direction. Having been an artist under the communist regime, it's extraordinary to me that people nowadays don't seem to appreciate their freedom as much as we thought everyone would. With the financial recession people are terrified of losing their jobs. They start to blame the EU's open borders and so on. At least with the Iron Curtain there was nowhere to go and nobody to take your job. So the fear brings out nasty xenophobia and anti-Semitism."

Fischer says that Hungary has a tendency to revert to racism, and that the current government has used such latent hatred to its political advantage. "I compare the country's racism habit to an alcoholic in a rehabilitation clinic," he says. "The former socialist government turned a blind eye when we fed our addiction; Orban's right-wing government feeds us the bottle." There is personal investment here: Fischer was born into a Jewish-Hungarian family, and much of his campaigning rallies against what he sees as increasingly accepted anti-Semitism in Budapest's upper echelons.

"Art in Hungary is paid for by the state," he explains, "and that creates a culture of artists who are dependent on the state and pander to it. Artists can't, or won't, bite the hand that feeds them. I resigned from the Hungarian State Opera because it was an administrative as well as an artistic role. Now I'm freelance and I can still conduct in Hungary, but I'm free to say what I like and other peoples' jobs don't depend on me. Those who can afford to should speak out for those who can't."

And Fischer can afford to. Along with his younger brother Ivan, the Fischers represent two of the most prestigious names in classical music. Ivan is the brilliantly flamboyant and innovative founding-director of the Budapest Festival Orchestra. Adam is a world authority on Haydn. In 1987 he set up the Haydn Festival at Eisenstadt (or "Haydnstadt", as it's nicknamed) – the great seat of the Hapsburg Eszterházy family who employed Haydn throughout most of his career) and the Austro-Hungarian Haydn Orchestra. He's a regular in Europe's finest opera houses – La Scala, Bayreuth, the Vienna State Opera – and principal conductor of the Danish National Chamber Orchestra.

Next week's concerts are his first collaboration with the SCO, a partnership that has all the requisite ingredients to produce serious sparks. On the programme is Haydn, Haydn and more Haydn: Fischer's speciality. He presents three of the composer's most celebrated late works – one sacred (the Nelson Mass), one operatic (Scena di Berenice), and one symphonic (Symphony No 101, the Clock).

Why the career focus on Haydn? "Actually it was an accident," he admits, with a laugh. "Though not an unhappy one. I went to my first concert when I was four, and I remember it well. It was a Haydn symphony. I loved his music from that moment. But the specialism I later developed was due to happenstance. Two years before the Iron Curtain came down I was contacted by Eisenstadt, which is so close to the Austrian border that nobody went there any more. The castle wanted to find a way of bringing visitors back." At first they set up a Haydn festival, then an orchestra for the festival, then a recording contract for the orchestra. By 2001 Fischer and the Austro-Hungarian Haydn Orchestra had recorded all 106 Haydn symphonies for a definitive 33-CD box set. "It's an exciting privilege to go through them all," he says, "and to be able to discover how the composer's ideas evolved. Usually we conductors have to spread ourselves too thin. Getting to know Haydn in such deapth has improved my work on other composers."

Incidentally, Fischer has recently taken a similar tack with Mozart, recording all of his symphonies and opera seria in Copenhagen. But the Haydn project has the added depth that comes with place. Eisenstadt is a bit like Wagner's Bayreuth: Haydn was so closely linked with the place that his music even shaped its architecture. "For example, he had the flooring changed from stone to wood," says Fischer. "Architects hate it because it's not conventional for the period, but musicians love it. There's a wonderful echo and warm sound. Just like learning Wagner operas at Bayreuth, if you learn to play Haydn at Eisenstadt you can memorise the sound and reproduce it in other surroundings."

When it comes to the mechanics of transporting that Eisenstadt sound to the Queen's Hall and City Halls, Fischer says he knows "80% of what I want from these pieces. I hope I can find solutions to the other 20% with the orchestra." Technical matters like where he asks violinists to position their bows, or whether the brass players should use natural or modern instruments–"these are things we figure out together. I don't like to go in with strict orders, it's the personality of the players I'm working with that counts."

Adam Fischer conducts the Scottish Chamber Orchestra at the Queen's Hall, Edinburgh, next Thursday and City Halls, Glasgow, on Friday March 1.