Following a high-profile data leak and a failure to communicate new grading scales, the final straw came when this year's German test included a 1947 text by German author Manfred Hausmann, who had worked for Nazi propaganda magazine Das Reich.
Students were asked to reflect on how "The Snail" - in which a gardener decides the pest has to die to protect his plants - dealt with questions about nature and life. The test omitted to mention the broader context of the author's Nazi past.
The case has caused embarrassment and anger in Austria, which was annexed by Nazi Germany into the Third Reich in 1938 and has been struggling for decades to escape a reputation for brushing its history under the carpet.
Salzburg educator Wolfgang Muehlbacher, part of a group of critical authors who exposed the incident, said a 15-member advisory panel of literature experts who picked the text had clearly missed its significance.
"I assume the people simply were not exact enough, took too little time for this so that they did not see what was going on," he said. "Former Nazis who were involved in this whole machinery of crime have to read the text as absolving them."
Hausmann died in 1986.
Education Minister Gabriele Heinisch-Hosek said the co-directors of the independent BIFIE institute in charge of overseeing educational quality and testing would go in July.
She convened an advisory panel to report back in a month on how the Alpine Republic can avoid such mishaps in future under a new leadership of the BIFIE.
The case has also raised renewed concerns that Austria's education system - while praised for its effective vocational training - is failing to equip young people with the academic skills they need to thrive in the modern world.
Unemployment is the lowest in the European Union but organisations including the Organisation for Economic Cooperation and Development group of wealthy countries have highlighted issues with Austrian schools.
"Austria's well-being model has largely drawn on the quality of its vocational education system, but the education system as a whole faces important challenges," the OECD found in its latest national survey of Austria.
It noted the proportion of students below minimum proficiency levels in international tests had risen while the share of those reaching the highest proficiency had fallen.Heinisch-Hosek promised a shake-up of BIFIE to ensure "less heads in the clouds and more feet firmly on the ground, less ivory tower and more suitability for practical use".