The 429 pieces were part of a collection belonging to a prominent French art dealer and collector, Ambroise Vollard, who died in July 1939 in an accident.
As World War Two broke out in Europe, part of his collection was transferred to Yugoslavian Erih Slomovic for safekeeping, but Slomovic, who was Jewish, was subsequently arrested and killed in a concentration camp in 1943.
The Yugoslav government later requisitioned the works and placed them in the national museum.
Lawyers for the plaintiffs say the museum, which has let some of the works be exhibited internationally, is well aware of their disputed history.
"The history of the 'Vollard/Slomovic collection' and the legal decisions rendered in France have created an international stir for decades and no curator or museum director holding these works could be unaware of it," wrote lawyer Francois Honnorat in the complaint filed on Wednesday, a copy of which was obtained by Reuters.
Another group of 190 paintings once owned by Vollard but left in Paris by Slomovic was similarly disputed in the courts, with the Vollard heirs ultimately winning an appeal in 1996.
The collection includes a trove of Impressionist and other 19th century art, including a still life by Paul Gauguin, lithographs from Paul Cezanne and Mary Cassatt, more than 50 pastels and drawings by Edgar Degas, and a group of works from Pierre-Auguste Renoir depicting women, dancers and guitar players.
Other great 19th and early 20th century painters whose works are found in the collection include Pierre Bonnard, Camille Pissaro and Maurice Utrillo.
The plaintiffs' lawyers say they had alerted the Serbian embassy in Paris to the litigation, but that it had not responded.
(Reporting By Thierry Leveque, Writing by Alexandria Sage, editing by Paul Casciato)