The Greens say the party leaders have repaid the bonuses and are cooperating with the investigation.
German prosecutors are probing the leaders of the Green party over allegations of paying out bonuses during the COVID-19 pandemic.
New vice-chancellor and finance minister Robert Habeck and foreign minister Annalena Baerbock are among those being investigated.
Berlin authorities are examing whether the party co-leaders approved a "corona bonus" of €1,500 each for themselves and all employees at the Greens' headquarters last winter.
The bonus was supposedly meant as compensation for having to work from home and during building renovations.
Prosecutors have confirmed launching an investigation into a breach of trust after a complaint by a private individual.
According to the DPA news agency, internal party auditors had already raised questions over the bonus payments to the leadership board.
The Greens party said its leadership was legally entitled to make the decision and has since paid the bonuses back.
"The affected board members and the federal office are cooperating fully with the public prosecutor's office to clarify the facts quickly and completely," a spokesperson said.
Both Habeck and Baerbock are expected to step down as party leaders now that they have taken on ministerial positions.
Baerbock's campaign for the German chancellery was damaged last year by the first reports of the bonuses, as well as revelations that she had failed to declare extra payments that her party had received between 2018 and 2020.