Katarzyna Wielga-Skolimowska was fired last week by the Polish Foreign Ministry, more than six months before her contract was to expire.
Rumours spread through the German media that Ms Wielga had upset the conservative Polish government by paying too much attention to Jewish-Polish issues and not enough to Polish-Ukrainian or Polish-Lithuanian dialogue.
The Jewish Museum in Berlin urged Poland’s ambassador to Germany, Andrzej Przyłebski, to rescind the decision.
The Polish Embassy has denied that Jewish programming had anything to do with the dismissal, and has demanded a correction and apology from two German newspapers.
However, in a private memo written in October, Mr Przyłebski criticised the Institute for spending too much time on Jewish-Polish themes.
Ms Wielga is not allowed to speak to the press until her employment officially comes to an end.
Observers say the real issue is not Ms Wielga’s coverage of Jewish topics but Poland’s shift towards ethno-nationalism.
Warsaw sent a new deputy director to work with Ms Wielga last spring. It was not long before this deputy, Małgorzata Bochwic-Ivanovska, was reportedly asked by Ambassador Przyłebski to screen a film about the 2010 plane crash that killed numerous members of the Polish conservative political elite, among them President Lech Kaczynski.
Ms Bochwic-Ivanovska reportedly could not find a venue in Berlin willing to screen Smolensk, which has been panned by film critics.
But Ms Wielga did hold a successful screening of Ida, the 2015 Academy Award-winner for best foreign film, which deals with the rediscovery of Jewish roots in Poland and the participation of some Polish Catholics in the extermination of Jews.