Fico and his former interior minister Robert Kalinak were charged on Wednesday and reportedly face up to 10 years in prison.
The former PM has denied any wrongdoing and dismissed the case as "clear political revenge" in an attempt to "liquidate the political opposition".
Fico is currently an MP for the opposition Smer-Social Democracy party, while Kalinask is employed as a lawyer.
Slovakian Prime Minister Eduard Heger said he hoped the autonomous decision to charge Fico and Kalinak was supported by evidence.
Fico twice served as the country's left-wing populist prime minister from 2006 to 2010, and again from 2012 to 2018.
He resigned after the 2018 murders of investigative journalist Jan Kuciak and his fiancee Martina Kusnirova.
Kuciak had been investigating possible government corruption when he was killed, and his death prompted unprecedented street protests and a political crisis that led to the government’s collapse.
The current Slovakian coalition had made the fight against corruption a key policy issue and a number of senior officials, police officers, judges, prosecutors, politicians and business people have been charged with corruption since it took office.
Police so far haven’t asked parliament to waive immunity rules and allow Fico's detention.