Enrico Saggese in a statement denied the accusations and said that he wanted to step down "so as to better defend my integrity, honour and prestige".
Prosecutors opened an investigation on Thursday into corruption, including Saggese's use of a credit card provided by an agency subcontractor.
They are also looking into consultancy fees paid to the wife of an employee to provide "psychological assistance" and expense-paid trips to the United States for several managers of the space agency.
Saggese has been head of the space agency since 2009 and the decision on whether or not to dismiss him is now up to Research Minister Maria Chiara Carrozza.
SEE ALSO: Italy to send first female astronaut into space
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