The questionable objects consist of 69 paintings, two sculptures, 31 decorative art objects, 13 Jewish ritual objects and 24 drawings.
The probe's findings were announced to coincide with the launch of a website (www.musealeverwervingen.nl) which details the objects and their histories, with the aim of getting help to complete missing information.
"The Museum Acquisitions research from 1933 gets to the heart of what museums do: studying their collections and telling the story to the public," said the association's director, Siebe Weide.
"It was no easy task, but our museums always realised the importance of the research. The fact that much time has passed since the end of the Second World War should not be a reason not to do the research," Weide said.
Included in the online list of potentially questionable artworks are Kandinsky's "View of Murnau with Church" and "Painting with Houses" as well as Matisse's 1921 "Odalisque".
Amsterdam's main modern art museum the Stedelijk has 16 questionable works, including the Matisse and Kandinsky's "Painting with Houses", while Amsterdam's celebrated Rijksmuseum has nine, including a 17th-century silver salt cellar by Johannes Lutma.
The Hague's main modern art venue, the Gemeentemuseum, topped the list with 19 questionable artworks, said a spokesman for the project who asked not to be named, declining to put a value on any of the works.
"The outcome was focused on getting into contact with the families, there's no amount to put on them," he said.
"The Kandinsky (at the Stedelijk) is of course an internationally known and pricey work of art but other works don't really have value moneywise, but might be important for family members," he said.
"The goal of the Netherlands Museum Association was really to go for transparency and really know what's happening in their collections."
Names of the original owners have been attributed to 61 objects, the association said, and owners can apply for restitution.
"Where possible the museums will try to make contact with relatives or heirs of the original owners," it said on its website.
The Nazis massively plundered artworks in Germany and across Europe before and during the Second World War, confiscating many from Jews or forcing them to sell their works at a low price.
The new research followed on from an initial 1990s probe into WWII acquisitions, after which it was decided to look at artworks' origins before 1940.
"The Netherlands felt increasing urgency over the last few years to obtain clarity about the origins of the public art collection, so that the right thing is done for victims of the Second World War," said Culture Minister Jet Bussemaker.
"Cultural assets can only prosper if there's openness and clarity about where the works come from," she said.