That a truly great historian of our times can, on very rare occasions, stumble into a meticulously laid trap is no more than to say that we are human and fallible. Or that water is wet. There are many points of view among historians, as there should be, about Hitler and Stalin and the comparative study of their evil works. Analogously, there are competing narratives about myriad aspects of the second world war – not least, the forever intriguing negative counterfactual of "What if it hadn't happened?" concerning the Ribbentrop-Molotov pact of August 1939, and, Hitler's attack on the Soviet Union in June 1941.

But a master historian, and Timothy Snyder is one of the best, always includes, almost as if by a higher inspired intuition, the key to unlock the very trap he may on a rare occasion be failing to avoid. In this case, it is the perspicacious line:

"Entering the lands that they had conceded to Stalin in 1939, the Germans used NKVD crimes as a propaganda justification for the bloody massacres of Jews in summer 1941, in which Lithuanians, Ukrainians, Poles and others took part."

What I have learned as a researcher of Yiddish who has lived in Lithuania for 11 years is that the obsession with finding some excuse – preferably that excuse – for massive local participation in the Holocaust is very much alive today among the elite classes of politicians, academics (especially historians) and media people throughout the region. And make no mistake, in the Baltics we are talking not just about "collaboration" with the Nazis, but "participation" in the frightening sense of thousands of volunteer killers being on hand to gleefully do most of the Nazis' killing, in effect of their own neighbours, in the three Baltic states and some other regions. At the same time, one must not for a moment forget the incredible courage of those Balts who did the right thing and saved a neighbour, notwithstanding the danger of imminent death to themselves and their loved ones.

After Baltic independence from the collapsing Soviet Union two decades ago, bold truth-tellers emerged to confront even the darkest spots of their nations' history. And which of our nations does not have dark spots? In the case of these long-suffering and newly independent states, it naturally took remarkable courage and a deeper love of country (and all the peoples of one's country) to tackle such painful matters head on.

But then, something went wrong. The three Baltic states in the late 1990s set up state-sponsored commissions to study Nazi and Soviet crimes, but not in an open and democratic spirit. This was a project of ultra-nationalist revisionism with an active political agenda that meant much more to the politicians than this or that historical volume produced for minute readerships. That political agenda was in short, to rewrite the history of the second world war and the Holocaust by state diktat, into a model of "double genocide". Holocaust denial was, in fact, never an option in a region with hundreds of mass graves. Instead, a new and more worrying "Holocaust obfuscation" movement took off, with a lot of government support in the region. It tries to reduce all evil to equal evil, in effect to confuse the issue in order to write the inconvenient genocide that is the Holocaust out of history as a distinct category.

The steps taken are eerily Orwellian in a well-planned sequence (but not, let it be stressed, a conspiracy: all of it was very public to anyone interested enough to follow events here in the Baltic region). The notion "genocide" was redefined by legislation to include deportation, imprisonment, loss of freedom and much more. This, then, made it possible (in local terms – necessary) to argue that, with the new definition in play, Nazi and Soviet crimes were obviously "equal". The "slight inconvenience" of the Holocaust then fades away naturally into the new grand paradigm of double genocide in which everybody was killing everybody, in the ultimate postmodernist mush.

Not to mention that the (understandably) Russia-fearing countries that were under Soviet yoke for so long are also not "uninterested" in a big new stick with which they hope to beat Russia down in western eyes to the status of a genocidal equivalent-to-the-Nazis regime. In other words, the policy is being driven not only by ultra-nationalism ("We have a perfect history"), antisemitism ("the Jews were basically communists and got what they deserve"), and anti-Russianism ("they are the same as Hitler"), but by a perceived set of current geopolitical concerns that should not (whether right or wrong) be converting history into a one-opinion discipline with the foregone conclusions being dictated by the state's apparatchiks.

Here in Lithuania, the powers-that-be have carried all this to absurdity. From 2006 onward, prosecutors, who had the most abysmal record of pursuing Nazi war criminals deported by the United States after extensive legal proceedings, somehow managed to find the energy to pursue Jewish survivors of the ghettos who fled into the forests to join the anti-Nazi resistance. There were no British or American troops in these parts, and yes, the Soviets were the only hope for the tiny number of escapees of the Nazi death machine during the years 1941-45 when the United States, Great Britain and the USSR led the allied coalition against Hitler. None of these Holocaust survivors was charged with anything specific – because there is nothing to charge them with. These were rather campaigns to change history, part of an expensive, extensive effort, slowly but surely, to change the narrative of history to suit the local ultra-nationalists.

It all reached a low point in May 2008, when police came looking for two women survivors in their late 80s, and prosecutors went on to tell the press that they could not be found. To this day, these kangaroo investigations have not been dropped, and there has still been no apology to the two women.

But that is not the half of it. In June of 2010, the Lithuanian parliament passed and the president shamefully signed into law a bill that would impose up to two years' imprisonment for anyone who might deny or underestimate Nazi or Soviet genocide. In other words, if a historian will say "Soviet crimes in Lithuania were horrific but they do not rise to genocide; there was only one genocide here, that perpetrated by the Nazis and their partners," he or she is potentially liable to prosecution. Now, Timothy Snyder would be the last to want colleagues of other opinions to have to pay for their ideas with jail time. (Ironically, just such things operated in the Soviet Union – and this is one of the examples of democracy deteriorating to something that is Soviet in form, nationalist in content, and conveniently western in its well-spun presentation to naive foreigners.) It is doubtful whether any historians will, in fact, be charged, tried or imprisoned. What the law has accomplished, however, is to silence nearly everyone into acquiescence to the state-imposed version of history. A very sad state of affairs in a European Union and Nato country.

But this is not a localised Lithuanian, or even a Baltic issue alone. It is part of a new far-right mood sweeping big swaths of the "new accession" states in the eastern regions of the European Union, a phenomenon elucidated by Paul Hockenos in Newsweek last October ("Europe's Central Disappointment"). In fact, the Lithuanian "jailtime-for-disagreeing-with-the-government-about-history law", though in the works for over a year, was only enacted right after the new rightwing government in Hungary enacted a similar law (the Hungarian statute imposes a maximum sentence of three years in jail).

But the rightwing-motivated revision of history (to downplay Hitler's role and play up Stalin's in order to wipe out the eastern stain of Holocaust participation) is no longer even just an east European game. Using newfound clout in the European Union, the nationalist camp has come up with a plan to get all of the European Union to accept their "double genocide" model. It started in a serious way with a conference in Tallinn, Estonia, in January 2008, ominously called "United Europe, United History", which promulgated the nonsense that the continent's unity depends on everybody accepting the same revised history of World War II and the Holocaust (in effect, Double Genocide), or else.

In June of that year, a much larger event produced the "Prague Declaration", which insists all of Europe agree that Nazism and Communism are a "common legacy" and that a Nuremberg tribunal-grade tool be used to assess communism. The revisionists want all Europe to enact a single commemoration day for victims of Nazi and Soviet crimes. Indeed, this would make the focal point of the second world war history the Ribbentrop-Molotov pact, by law rather as a matter of opinion, and of necessity relegate Holocaust commemoration day rapidly to oblivion. Back to Soviet-style mind control, the declaration even demands an "overhaul of European history textbooks" to reflect the revised red-equals-brown history. For shame.

Now Professor Snyder is absolutely right to call for a much-increased attention to the lands occupied by the Nazis after their June 1941 invasion of the western Soviet Union, where a million Jewish civilians were murdered, with massive local help, by the end of 1941 in "the Holocaust by bullets". But where he is unfortunately aligned with the current political trends into the far-out is in the acrobatics of trying to make Soviet evils of 1940-41 "somewhat equal" to that. They are not equal.

The Estonians, Latvians, Lithuanians, Poles and Ukrainians are still thankfully with us in 2010, as great nations with deservedly inspirational futures, precisely because there was no genocide. There were horrible crimes, but not genocide. East European Jewry is not there anymore, beyond a tiny and vanishing remnant, because there was genocide. Moreover, as Snyder must know, a Nazi victory in the east, with all that was being planned for the various "inferior races of the east" would not have left these nations ready for independence in 1991.

Lithuania's one Liberal MEP in the European parliament, philosopher Leonidas Donskis, an incalculable credit to his country and all Europe, has exposed the "Inflation of Genocide" as a semantic and philosophic lynchpin of the series of errors and deceptions underway. I then proposed this definition:

"Genocide is the mass murder of as many people as possible on the basis of born national, ethnic, racial or religious identity as such; with intent to eliminate the targeted group entirely and internationally; without allowing the victims any option to change views, beliefs or allegiances to save themselves; and with large-scale accomplished fulfilment of the goal. Genocide leaves in its wake an extinct or nearly extinct group within the territory under the control of the perpetrators."

Returning to the actual history of the second world war, Snyder, turning to the important point of local collective memory, happens to be in concord with the Baltic ultra-nationalists who want the Molotov-Ribbentrop pact, rather than the genocide of the Holocaust, to be the psychologically central sin of the century; to be sure, the master historian and the local nationalist hijackers of history are coming to it with altogether different tools and motives. But what I can testify, after many years of talking to Lithuanians, Latvians, Belarusians, Poles, as well as Jews, is that, believe it or not, there is a common memory of the war here having started in 1941 – while the events of 1939 continue to be recalled as a nearly bloodless changeover of regimes that was either despised or cherished depending on one's ethnicity (as politically incorrect as that may sound).

And finally, it is not possible to ignore Snyder's certainty that "Jews could not help but see the return of Soviet power as a liberation. Soviet policy was not especially friendly to Jews, but it was obviously better than a Holocaust." The liberating power was, in short order, to become an oppressive power, as has happened not once but many times in history. But in 1944, the USSR did liberate these lands from Nazi dominion, and they did bring freedom to the tiny remaining remnant of the targeted-for-extinction races. From the day the Holocaust started here, in June 1941, the Soviets were often the only hope of escape for members of a doomed race, whether by fleeing eastward before Nazi control was firmly established in the first week after 22 June that year, or, by evading the ghettos to link up with the Soviet supported anti-Nazi partisans in the forests.

Genocide is different from the other crimes of the era, and for this reason, the Holocaust was unique, not just for Jews but for all peoples of good will who want to prevent other genocides in the future. It is, moreover, frankly possible and even constructive for the surviving majority, restored to deserved independence and membership in the greatest unions of democratic states in history, to show non-ethnocentric understanding about the genocide of a minority that had contributed mightily to their country for some six centuries beforehand.

It is strange how things have moved so far down the track, with a massively financed effort by east European governments to cleanse their Holocaust records with a bag of sophisticated artifices, to the point out that even great scholars can sometimes fail to see something very simple: those who liberated Auschwitz (or for that matter, the lands of eastern Europe) are just not the same as those who committed the genocide here. Period.