VILNIUS, Lithuania — During the Holocaust, many Lithuanian Jews were not killed in Nazi death camps, but by their neighbors, usually shot or even beaten to death. In all, 90 percent of an estimated 250,000 Jews perished, wiping out a community that had been part of Lithuanian life for five centuries.

So it may come as a surprise that in Vilnius, the country’s capital, there is a thriving Jewish community center (including a cafe serving bagels), an expanded new Jewish Museum and fully functioning synagogue — beneficiaries of a Western-looking government that encourages Litvak Jews to return and has proposed to declare 2019 “The Year of the Jew.”

In the Ponary neighborhood, on the outskirts of town, there is a memorial, which eventually included the 70,000 Jews who were stripped naked and shot to death in the forest there. And in the city, there is a huge Museum of Genocide Victims.

That, however, is where the glowing picture suddenly becomes murky.

Until recent years, the museum, in what was once the headquarters for the Nazi S.S. and later the K.G.B., the Soviet secret police and intelligence apparatus, did not even mention the Holocaust, in which the German Nazis used Lithuanian partisans and police to round up and kill the country’s Jews.