The Viola paid for airline tickets for Berbatov to come to Florence, undergo his medical and complete his move from Manchester United just two days before the end of the summer transfer window.
However, the Bulgarian striker did not travel to Italy and eventually signed for Fulham instead, with Fiorentina claiming that he broke a "verbal agreement".
"We will ask his attorney for a refund for the tickets paid," Viola sporting director Daniele Prade told Radio Blu.
"I'm glad he did not arrive in the end. It is better this way. In my 25-year career in this business, I have never seen anything like this.
"We will see if there is something in the market to our liking. We are not desperate for a new striker, for we have Luca Toni now who will be a real asset on and off the field."
Berbatov signed a two-year contract with Fulham.