Mr Francken filed the complaint last October after the youth section Ecolo J published a photo montage of the Flemish nationalist in a German Nazi soldier's uniform and brandishing a gun. The photo formed part of protests against co-operation between Belgium and Sudan in the identification of migrants in the Maximilian Park in Brussels, where many migrants are encamped.
Mr Francken first demanded an apology. When this was not forthcoming he filed a complaint with the judicial authorities.
The complaint has now been subpoenaed "as it's not a priority".
Mr Francken responded: "A sad state of affairs. A party portraying a colleague as a Nazi soldier with a gun can't be justified."
Brussels prosecutors clarified: "The protest hasn't been dismissed for good. If prosecutors receive fresh information, it can be reopened or a civil action can be initiated."