Launched in 2017 to replace France's Rafale jets and the Eurofighter planes used by Germany and Spain, FCAS is being jointly developed by Paris, Berlin and Madrid.
However, the project has been stalled by tension between the main industrial partners, France's Dassault and Airbus, which represents German and Spanish interests.
According to the German Hartpunkt news site, France wants to be in charge of around 80 percent of the work on the project.
Pistorius, speaking alongside his Spanish counterpart Margarita Robles on Thursday, said that "national interests will have to be put to one side" in order to move forward with the project.
"We have agreed that all three FCAS countries will meet here in Berlin in October to analyse" how to move forward, "to identify the traps and how to remove them," Pistorius said.
Dassault has said that it wants the agreements over the project to be revisited so that it can have a free hand in choosing its subcontractors.
Pistorius said on Thursday that "agreements are made to be respected" and could only be modified "after fresh negotiations between the parties to the contracts".
But he stressed that "the project cannot tolerate any more delay".
German Chancellor Friedrich Merz said last month he was "confident" that the difficulties in the project could be overcome.
On Thursday he will meet French President Emmanuel Macron, a day before a joint Franco-German ministerial council in Toulon.
jpl-jsk/fz/giv
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