The former Secretary Horace Engdahl wrote an open letter to the Swedish daily Expressen on Tuesday, calling Danius the worst Secretary since the foundation of the Academy in 1786. The institution, which awards the Nobel Prize for Literature, has come under fire for its handling of a sex abuse scandal.
The Nobel Foundation Board has sharply criticized the Swedish Academy, which chooses the Nobel Literature Prize victor each year, for damaging its own reputation and threatening to tarnish the reputation of the Nobel Prize itself.
"It was the wish of the Academy that I should leave my role as Permanent Secretary", Sara Danius told reporters.
"Confidence in the Swedish Academy has been severely damaged", the Nobel Foundation, which manages the financing and administration of the Nobel Prizes, said on Wednesday in an extraordinary public rebuke.
Until a replacement is found, Anders Olsson, who has chaired the academy's meetings this term, will replace Danius. Unlike Swedish Radio, Reuters published the identity of the man and the Academy member as Mr. Jean-Claude Arnault and Mrs. Katarina Fronstenson.
Even before last week, two of the academy's 18 members long ago stopped taking part and have not been replaced: One left in 1989 as part of a protest over the academy's response to threats made against the writer Salman Rushdie, and another stopped taking part in 2015, saying that she did not feel she fit in.
In his second statement this week, Carl XVI Gustav, said that "it is crucial that all involved now realize their responsibility for the institution and contribute to resolving conflicts". Members are appointed for life and can not technically resign.
With Thursday's announcement, seven of the academy's 18 members have stepped down, casting doubts as to whether the organization can function properly. However, there is nothing forcing them to actively participate if they choose not to do so.
In an emailed comment to Reuters on Thursday, Arnault's lawyer, Bjorn Hurtig, said his client rejected all allegations against him. Her husband, Jean-Claude Arnault, denies the allegations against him. You can sign up to receive it directly here.