A pair of Bavarian tourists photographed the paintings during a 2007 visit to Ukraine's Crimea province and sent copies of the shots to the Aachen museum after finding the paintings listed as "whereabouts unknown" on the Aachen museum website.
The art works, reportedly mostly by Western European artists, had been transferred from Aachen to the German city of Meissen for safekeeping in 1942 and had been thought to have been lost or destroyed during the later Allied invasion of Germany.
According to the tourist, one painting featured an image of the inner court of Nuremberg's St Lorenz church and a still-legible German inscription on the frame identifying the work as part of the Aachen collection.
Meissen was in the Soviet zone of control during Allied occupation of Germany.
"It is explicit, here (in the Simferopol museum) were on display 87 paintings from Aachen's Suermondt-Ludwig Museum," said Philip Becker, curator of the museum's current "Schattengalerie" exhibition.
"They (the paintings) can no longer be put on display, because the question of restitution (of the paintings to Germany) has not been resolved on the governmental level."
Disputed paintings at center of ownership row
Text descriptions accompanying the exhibition in Ukraine gave the "false impression" that the current ownership of the paintings had been resolved and that the Simferopol museum had full right to display the art works, Becker claimed.
The Aachen museum was "astounded" at the find and had no early plans to recover the paintings, he added.
Simferopol's spokeswoman told reporters the museum had no intention of returning the paintings.
The museum's management reportedly justified the intention not to give up the paintings, citing a Ukrainian law giving people or organizations having suffered property damage during the German invasion of the Soviet Union during WWII legal title to German property captured by Red Army troops in later stages of the war.