Tytti Yli-Viikari, who was dismissed from her role as auditor general by Parliament in June, has been charged with aggravated abuse of office.
Another employee of the National Audit Office (VTV), the agency's director Mikko Koiranen, has also been charged with the same crime.
The charges relate to an agreement between Yli-Viikari, Koiranen and an agency official, in which the official received a salary for two years despite having no work obligation.
Finland's Parliamentary Ombudsman has declared the agreement illegal.
Yli-Viikari also faces charges of payment fraud and misconduct in a public office over the use of Finnair Plus bonus points.
The charge is related to Yli-Viikari's suspected use of frequent flyer bonus points — accumulated from business trips — for her own personal trips, even though the points belonged to her employer.
Yli-Viikari has denied the charges and has also appealed her dismissal from the role of Auditor General to the Administrative Court.
Koiranen, who is currently suspended from his position with the VTV, has also denied having committed any crime.