Magistrate Natasha Galea Sciberras will lead an inquiry into claims that the Prime Minister's chief of staff Keith Schembri received kickbacks from the sale of passports.
The magistrate was selected by lot, as required by law.
Allegations concerning Mr Schembri were first brought before Magistrate Aaron Bugeja, the inquiring magistrate leading a probe into Egrant claims, by Opposition leader Simon Busuttil.
Magistrate Bugeja decreed that the allegations should be the focus of a separate inquiry.
In a brief statement issued by the Office of the Prime Minister, Mr Schembri said he had "absolute confidence" in the judiciary, would be cooperating fully with the inquiry and "looks forward to having the opportunity to expose the whole truth."
Dr Galea Sciberras was appointed a magistrate in 2012. Born in 1976, she graduated as a lawyer in 2003.