A Russian historian investigating the fate of Germans imprisoned in the Soviet Union during the second world war has been arrested, in the latest apparent clampdown on historical research into the Stalin era by the Russian authorities.

Mikhail Suprun was detained last month by officers from Russia's security services. They searched his apartment and carried off his entire personal archive. He has now been charged with violating privacy laws and, if convicted, faces up to four years in jail.

Suprun had been researching Germans sent to Russia's Arctic gulags. A professor of history at Arkhangelsk's Pomorskiy university, his study included German prisoners of war captured by the Red Army as well as Russian-speaking ethnic Germans, many from southern Russia, deported by Stalin. Both groups ended up in Arkhangelsk camps.

"I had been planning to write two books. I need another two or three years before I can finish them," Suprun told the Guardian today. The historian – who described his arrest as "absurd" – said he had signed an agreement with local officials not to talk further about his case.

But the arrest has provoked outrage in Germany and among leading historians. It comes amid Kremlin attempts to rehabilitate Stalin and to clamp down on independent historical research – with political repression during the Soviet era and victims of the gulag system now taboo topics.

Today the historian and writer Orlando Figes described Suprun's arrest as unprecedented, and part of a "Putinite campaign against freedom of historical research and expression". Figes, professor of history at Birkbeck college, London University, added: "[It's] potentially quite alarming, if it means that the regime intends to clamp down on the collection of personal data about the Stalin terror."

Suprun's project was done in collaboration with Germany's Red Cross. The organisation is still trying to establish the fate of thousands of Germans transported to Soviet Russia as prisoners during the war – many of whom never came back. The German Red Cross today said it was baffled by the historian's arrest. It was "completely unacceptable", Erica Steinbach, a rightwing German MP, added.

Russia's FSB intelligence agency also arrested a police official who handed Suprun material from the local interior ministry archive. It includes a list of 40,000 German gulag victims between 1945 and 1956, deported to the Arkhangelsk region. It details which camps they were sent to and whether they survived. The official, Col Alexander Dudaryev, is accused of abusing his position.

"What we are seeing is the rebirth of control over history," said Rauf Gabidullin, of Arkhangelsk's movement for human rights. "The majority of Russians don't have any idea of the scale of Stalin's repression. Those in power are from the KGB. They don't want people to know what their KGB predecessors were doing, or its huge scope."

Asked what life was like in Arkhangelsk's freezing gulags, overlooking the White Sea, he said: "Terrible. The winter was extremely long. The conditions in the barracks were appalling. The German prisoners who were lucky enough to survive chopped wood. In other parts of the Soviet Union they constructed buildings, including Moscow state university."

The Arkhangelsk camps also contained Poles, Greeks, Tartars and other non-Russian ethnic groups. By the end of the war 11 million Germans were in allied prison camps. More than a million perished. Soviet prisoners of war fared even worse. Of the 5.7 million taken prisoner in Germany 3.3 million died – more than half.

The second world war remains a source of major tension between Russia and its post-Soviet neighbours. Russia's president, Dmitry Medvedev, has repeatedly accused Ukraine, Poland and other eastern European countries of distorting history for political purposes and in May set up a new state commission to prevent what he called the "falsification of history".

Over the summer Moscow reacted furiously when the Organisation for Security and Co-operation in Europe's parliamentary assembly, led by the Baltic states, passed a motion equating Nazism with Stalinism. The Kremlin has also defended the Molotov-Ribbentrop pact – under which Stalin and Hitler carved up eastern Europe – describing it as a tactical agreement no different from other western accommodations with the Nazis.

Today Allison Gill, the director of Human Rights Watch in Moscow, described the Suprun case as "very troubling". "It's part of an attempt to provide a single narrative about what Russia was, and what it means today. It denies the full complexity of Russia's history and the fact that individuals had vastly different experiences. I don't like it at all," she said.

Suprun's research is similar to several other projects carried out over the past two decades by the Russian human rights organisation Memorial. Memorial has collected the names of tens of thousands of gulag victims, publishing their details in public "memory books". Last year police raided Memorial's office in St Petersburg office, seizing material used by Figes in his book on family life in Stalin's Russia, The Whisperers. They later returned it.