The investigation is yet another complication in the merger between Porsche and auto powerhouse Volkswagen.
The three employees, who remain unnamed, are accused of lying to a bank about the number of options Porsche held on VW ordinary stocks in 2009, when Porsche was in talks about the refinancing of a €10 billion loan.
When the bank questioned Porsche about its financial needs during negotiations, the three suspects undervalued the options by around €1.4 billion.
The luxury car company had run up millions in debt whilst unsuccessfully trying to buy VW.
Whether or not the three suspects are still employed at the firm is unknown, but they are also facing charges of embezzlement and market manipulation, state prosecutor Claudia Krauth said in a statement.