According to the charges, Reps committed embezzlement when she instructed ministry employees to carry out childcare duties for her children while working as a minister.
Reps was charged with illegally using the ministry's fuel card and having the ministry pay for her birthday party which took place on the ministry's premises.
She was also charged with fraud. The ministry bought a coffee machine for Reps' home, paid for family travel expenses, transport and accommodation in relation to a leisure event, and paid for a birthday celebrated at a restaurant.
The charges point to approximately €7,500 being misused.
Public prosecutor Denis Tšasovskih said every civil servant has a duty to ensure that state assets are used for their intended purpose.
"Legislation applies to everyone and a high position in the civil service hierarchy does not give anyone the right to bend these norms in a self-serving way," he said.
Proceedings were initiated after newspaper Õhtuleht published a story alleging the misused of ministry money last year.
At the end of October, the Riigikogu waived Reps' right to parliamentary immunity so court proceedings could be started. She is still a serving member of the Riigikogu.
She has been a member of the Center Party since March 1998 and a minister multiple times.