Franz Allert's resignation late on Wednesday came shortly after the German capital's mayor Michael Müller made an open call on public broadcaster RBB for "new leadership for Lageso".
Known by its acronym Lageso, Berlin's State Health and Social Office is migrants' first port of call in the German capital.
Since June, hundreds of men, women and children have queued and jostled almost daily in its unsheltered dirt courtyard, some of them for weeks, waiting for a number and an initial interview with a frazzled bureaucrat inside.
But activists at Moabit Hilft, one of the groups which has organized grassroots support for the refugees waiting at the Lageso, don't believe the change of leadership will help them.
"Of course we don't expect anything to change. The fish stinks from the head down – the [Berlin] Senate is responsible for the situation," Moabit Hilft spokeswoman Diana Henniges told The Local.
She argued that the city needed to send more experts to organize humanitarian and medical aid – and call in outside help to restructure the inefficient bureaucracy at the Lageso.
As the weather gets chillier, she said, the situation will inevitably get worse.
"People are out on the street in the cold, and they are hungry because they don't have any money. It's down to two degrees and it might snow next week," Henniges said.
The poor conditions outside the Lageso have meant that security guards, backed by police, have sometimes had to contain the crowds as scuffles have broken out.
Neighbourhood volunteers like those organized by Moabit Hilft have so far averted disaster by handing out clothes, warm drinks and food as the weather turned colder.
Lageso was also where a four-year-old Bosnian refugee was kidnapped and later raped and killed by a paedophile who apparently took advantage of the chaos at the site.
Germany is expecting to record one million in asylum seeker arrivals this year, and Berlin has registered 70,000 newcomers since January.
Despite volunteers' best efforts, the situation is "shocking and unworthy of a democratic society," charged the Green Party's parliamentary vice president Claudia Roth.
In an open letter to Berlin mayor Martin Mueller, she said she saw people "endure the queues, sometimes in the mud, rain and storm, often tightly packed into closed-off ares, tents or buildings, with no guarantee that their suffering will be worth it".
Many of the refugees, Roth wrote, "feel powerless, helpless and as if trapped in a nightmare".
Roth said that in her southern German home state of Bavaria - where conservative politicians have railed the loudest against the influx – the on-the-ground aid efforts had nonetheless been far more professional.
This was despite the fact Bavaria is taking in 15 percent of refugees coming to Germany, against five percent for Berlin.
Highlighting the chaos has been the tragic case of four-year-old Bosnian boy who was kidnapped from the crowd and killed by a serial offender.
Mueller defended his city's efforts, pointing to the "special situation" and ongoing efforts to expand staffing and services, adding that "the topic of housing refugees should not be used for political games".
Meanwhile, over 40 lawyers have filed a criminal complaint against the city's health senator Mario Czaja, alleging the institutional neglect was "causing bodily harm".
"In no other state are politicians and administrators failing as systematically as here," charged lawyer Christina Clemm, claiming the result was injuries, illnesses, hunger and homelessness.
Tensions in refugee camps
Another Berlin flashpoint has been a vast refuge shelter set up, months after the idea was first floated, in the massive Nazi-era Tempelhof airport, which during the Cold War served as a crucial western military air hub.
The mood inside has been described as tense, in part because 2,200 inhabitants in bunk beds have to use outside portable toilets and a bus shuttle service to take showers in nearby public swimming pools.
"These are inhumane housing conditions," a volunteer told AFP, speaking on condition of anonymity. "There are children who have scabies but receive no medical treatment and continue to play with others."
In late November, tensions escalated at Tempelhof and groups attacked each other, some armed with metal rods and knives.
Berlin, faced with a chronic housing shortage, plans to expand the Tempelhof site and accommodate up to 8,000 people in tents inside its hangars.
The Berliner Zeitung daily said the challenge was to build a functioning refugee facility "akin to a small town".
"The experiment at the airport, which once stood for the defence of freedom, must succeed," it said.
"Otherwise there is a danger that Tempelhof will be mentioned in the same breath as the infamous Lageso. It would be proof yet again of the government's failure," added the daily, referring to the registration centre.
Tom Barfield contributed reporting