The German Interior Ministry on Thursday announced the resignation of Manfred Schmidt, the head of the Federal Office for Migration and Refugees (BAMF) for personal reasons.
The BAMF has been criticised recently for working slowly to solve the refugee crisis.
It has said that there are more than 250,000 asylum applications waiting for the BAMF to decide upon with an average processing time of over five months. The turnaround time in the Netherlands, Germany's neighbor, is an average of eight days, according to Deutsche Welle.
The loss of the head of the BAMF in a time of an expanding refugee and migrant influx increases the burden on German Interior Minister Thomas de Maiziere.
"The interior minister regrets the loss of the head of an authority who performed an excellent job," a Ministry statement said. “The dramatically rising number of asylum seekers in Germany poses enormous challenges to the Office as well as to Germany's states and municipalities."
Schmidt had been in office since 2010.
De Maiziere thanked Schmidt for his "extraordinary work" at an extremely difficult time. He hasn’t announced a replacement yet.
Since Sunday, Germany has temporarily implemented border controls with its neighbours - first with Austria, then the Czech Republic, although these are included in the Schengen zone for unrestricted travel within EU borders.
German police have said the number of refugees is rising again. Over 7000 refugees arrived in Germany on Wednesday, more than double the previous day’s 3,442.
Germany expects between 800,000 to 1 million refugees to arrive in the country this year, which is almost the sum of the number to arrive in the previous five years.