The works were believed to be worth a combined $163 million.
The Washington Post described it as Switzerland's biggest art robbery.
Swiss police said Tuesday two of the purloined paintings -- Monet's "Poppies near Vetheuil" and van Gogh's "Chestnut in Bloom" -- were discovered by a parking lot attendant Monday in an unlocked car outside the University of Zurich Psychiatric Hospital, the Post reported.
"I am incredibly relieved that two paintings have returned," Museum Director Lukas Gloor told reporters Tuesday. "We're very happy that both the paintings are in absolutely impeccable shape."
"We don't know if the other two paintings are still in the country," Zurich police spokesman Michael Wirz told the Post in a phone interview. "The only thing I can tell you is that the robbers were not stopped, and we are still looking for them."