It is a small operatic gem that was written under torturous circumstances and almost failed to see the light of day when its composer was dragged off to the gas chambers before being able to hear it performed. But it lives on thanks to a professor of philosophy who survived Theresienstadt concentration camp, where it was written, and who preserved the manuscript.

Now a Berlin orchestra and an American conductor are to revive The Emperor of Atlantis by Czech-German composer Viktor Ullmann on a more than unusual stage – the former headquarters of the SS and Gestapo in the German capital, known as the Topography of Terror. "We wanted to reinforce the immediacy of the genocide of Ullmann and whole schools of composers of that time and this is a far more effective mise en scène than an opera house would be," said John Axelrod, the US conductor who is leading the project.

Ullmann, who was Jewish and had been a pupil of the Austrian composer Arnold Schoenberg, wrote the operatic satire on Adolf Hitler knowing full well that it would lead to his death. The nature of its contents was not lost on the SS authorities of Theresienstadt, who soon after the final rehearsal of the work, in March 1944, deported Ullmann to Auschwitz, along with his librettist, Peter Kien, where he was murdered on 18 October aged 46.

"Ullmann clearly set out to make an anti-Nazi piece, in which art should hold up a mirror to what the Nazis were doing," said Axelrod, in between rehearsals with the musicians from the Kammersymphonie Berlin. The one-hour opera is an energetic mix of jazzy interludes, touches of cabaret, Bach-style chorales and sweet lyricism. It serves, according to Axelrod, as a bittersweet tribute to the long lineup of musicians whose murder or expulsion from Europe "destroyed much of the continent's musical legacy".

He points to the direct cribbing in Ullmann's opera of many of the works of the great composers of the German-speaking world who were either classified as degenerate because of their Jewishness by the Nazis and their music banned – as was the case with Mahler, Mendelssohn and Weill – or whose music was commandeered for propaganda purposes, such as Brahms or Wagner.

"He's using the opera to ask, what happened to German enlightenment and its key ideal, all people become brothers?"

Like many musicians, Ullmann, who was considered one of the leading composers of his day, was sent to Theresienstadt in what is now the Czech Republic. The concentration camp was presented to the outside world as a pristine model fortress town whose "inhabitants" – so Nazi authorities were keen to show – were treated decently, to the extent that they were able to carry on their musical, acting or artistic careers. In reality tens of thousands were murdered there and for more than 150,000 others it was a holding camp from which they were taken by rail transport to death camps elsewhere.

At a rehearsal this week on Friday, the somewhat unusual array of instruments in the orchestra, including a guitar, banjo and saxophone, poignantly reflected the fact that Ullmann had to write his opera around whatever musicians were available to him in the camp.

Despite his musical prominence in his lifetime, most of Ullmann's music was lost during the Nazi occupation of Czechoslovakia. That The Emperor of Atlantis survives at all is thanks to Emil Utiz, a Prague professor who was Theresienstadt's librarian and took the score out of the camp when it was liberated.

It was first performed in Amsterdam in 1975, parts of it having been lightly edited after a spiritualist who claimed she could contact dead composers said she had received communication of the changes directly from Ullmann.

• This article was amended on 31 May 2013. The original said that there are no female voices in the cast, and that Eva Braun is represented by drums. There are in fact two female roles: a soprano (The Maiden) and a mezzo-soprano (The Drummer). The Drummer represents Eva Braun. These references have been removed.