Prime Minister Tony Abbott has made long-time public servant and former Labor staffer Michael Pezzullo secretary of the Department of Immigration and Border Protection, starting on October 13.
Mr Pezzullo joined the public service 27 years ago and is currently the chief executive of the Australian Customs and Border Protection Service.
"He has extensive experience in the public sector, predominantly in the Department of Defence in strategic policy and intelligence roles," Mr Abbott's statement said.
He worked as an adviser to former foreign minister Gareth Evans and was deputy chief of staff to the then opposition leader Kim Beazley.
Mr Pezzullo will replace Martin Bowles, who was recently appointed Health Department secretary.
In a note to staff regarding the case involving his brother, Mr Pezzullo later said: "From the outset, I asked and expected to be treated as a detached family member with no official rights, interests or powers in the matter."
Former ACT Policing boss Roman Quaedvlieg - Customs' current deputy chief executive - will become head of the agency.