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 yesterday 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.