"Gurlitt: Status Report", which displays around 450 pieces by masters including Monet, Gauguin, Renoir and Picasso, aims to shed a light on the systematic looting of Jewish-owned collections under Adolf Hitler.
The works in the two exhibitions, which run in Bern and the German city of Bonn until March, derive from the more than 1,500 discovered in 2012 in the possession of Munich pensioner Cornelius Gurlitt.
His father, Hildebrand Gurlitt, worked as an art dealer for the Nazis starting in 1938.
"With these two exhibitions, we wish to pay homage to the people who became victims of the National Socialist art theft, as well as the artists who were defamed and persecuted by the regime as 'degenerate'," Rein Wolfs and Nina Zimmer, directors of the Kunsthalle Bonn and the Kunstmuseum Bern, respectively, said in a statement.
The discovery of the stash made headlines around the world and revived an emotional debate about how thoroughly post-war Germany had dealt with art plundered by the Nazi regime.
The show, split between the two museums, is the result of years of disputed research into Gurlitt's collection, which was discovered in the course of a tax probe.
Inspectors found the works in Gurlitt's Salzburg home and his cluttered Munich apartment, many in poor condition, unframed and mouldy.
- Legal tangles -
Gurlitt, who died in 2014 at the age of 81, was described in the press as a recluse who lived off the sale of pieces from his collection, valued in the millions of euros.
The exhibition in Bern focuses on modern works which were classified by the Nazis as "Degenerate Art" in 1937 and confiscated for sale abroad.
In Bonn, the show will present art that was looted from victims of the Nazi regime and works whose provenance has not yet been established.
The exhibits themselves have prompted difficult legal tangles.
When Gurlitt died he left the more than 1,500 artworks to the Bern museum.
The Swiss museum accepted the collection, though it left about 500 works in Germany so that a government task force could research their often murky origins.
But determining their provenance has been slow, and it is not yet clear how many of these works were stolen.
Researchers have definitively identified just six works of art as looted from Jewish owners.
Zimmer told AFP at a packed press preview of the Bern exhibition featuring about 150 works that she was hopeful for more clues to the collection's provenance by the end of the year.
"I think we will be busy with research on Gurlitt for quite some time," she said.
- Cezanne behind a cupboard -
Four works, including Max Liebermann's "Two Riders on the Beach" and Henri Matisse's "Seated Woman", have now been returned to their former owners' heirs.
And last week, authorities said they had identified a painting by Thomas Couture as belonging to French Jewish politician and resistance leader Georges Mandel.
Other families have also tried to lay claims to works.
Relatives of Paul Cezanne have asked for the return of "La Montagne Sainte Victoire," a painting found in Gurlitt's Salzburg house behind a cupboard.
Andrea Baresel-Brand, director of the Gurlitt Provenance Research Project, said she hoped that exposing it to a large audience would lead to the identification of more rightful owners.
"Maybe somebody will recognise something or he will remember that in a suitcase in the attic there is a letter by his aunt where she talks about an artwork, so we are really hoping we will have feedback," she told AFP.
Meanwhile the World Jewish Congress president Ronald Lauder criticised the continuing failure of many German museums and private collectors to comb their own works for looted art.
"There are still museums and collection that do no provenance research at all," he told weekly newspaper Die Zeit.