Reinhard Boos, the head of the secret service bureau in the eastern state of Saxony, resigned in an affair that last week claimed Germany's domestic intelligence chief after his office admitted to shredding key files.
Heinz Fromm, president of the Federal Office for the Protection of the Constitution (BfV), resigned last week after 12 years in charge while the leader of Thuringia' bureau, Thomas Sippel, was also dismissed.
The Thuringia bureau has been branded the "chaos office" by German media this week, following testimony from Sippel's predecessor Helmut Roewer, who was reportedly prone to revealing confidential information in his office during impromptu wine and cheese parties.
A colleague also testified that during his tenure from 1994 to 2000, Roewer wandered around the office barefoot, chatted about top secret sources in the kitchen, and once rode a bike around the sixth floor of the building.
Roewer himself testified he was too drunk to remember who handed him the envelope that contained his own appointment in 1994.
Roewer was still in charge when the neo-Nazi terror trio Uwe Mundlos, Uwe Böhnhardt und Beate Zschäpe disappeared in the late 1990s before their murder series began.
Saxony's Interior Minister Markus Ulbig said that the state security services had only recently learned that they had transcripts from wiretapped telephone calls related to the neo-Nazi probe dating from 1998.
"The reason this fact only came to light now is apparently linked to the gross misconduct of individual staff members," Ulbig told the state legislature.
"The president (of the Saxony state intelligence service) deeply regrets this occurrence which is why he has asked me to give him another post from August 1 of this year."
Ulbig said he had ordered the transcripts to be reviewed and sent to federal prosecutors to aid their ongoing investigation of the murders, mainly of Turkish-born shopkeepers throughout Germany between 2000 and 2007. Boos had led the office since 2007 and also between 1999 and 2002.
It emerged in November that a far-right trio calling itself the National Socialist Underground (NSU) was likely behind the murder spree.
The case broke open only when two members of the NSU were found dead in an apparent suicide pact and the other, a woman, turned herself in.
Investigators initially suspected criminal elements from the Turkish community were behind the rash of killings in a probe marked by repeated missteps and allegations of a cover-up.
A parliamentary committee is investigating the affair and the German government has pledged a root-and-branch reform of the security services.