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The 31-year-old had also been linked with a move to Italian champions Juventus and English Premier League club Fulham, the BBC reported on Thursday.
Fulham declined to comment on the speculation, the BBC said, and Juventus director general Giuseppe Marotta refuted Fiorentina's accusations.
"We have acted with the maximum fairness and transparency with regard to the market dynamics," Marotta was quoted as telling Sky Italia.
"I reject the allegations from Fiorentina. We entered into the business over Berbatov when we heard that he had refused Fiorentina, and in the meantime there was a proposal by Fulham.
"We made our own, then the player said he preferred to stay in England for family reasons. It was not a rejection. We wanted to take advantage of an opportunity that had appeared to us in the market."
Bulgaria striker Berbatov, who came to United in 2008 but struggled to hold down a place in the first team last season, had been expected to join Fiorentina subject to a medical.
"The player embarked in the company of his agent and with tickets paid by Fiorentina on a direct flight to Florence," the Serie A side said late on Wednesday. "But the player never arrived in Florence.
"(This was) owing to the reckless and arrogant actions of other clubs which have nothing to do with the values of decency, fair play and ethics of the sport and which go beyond the limits of fairness.
"As for the player, notwithstanding his characteristics and technical merit, at this point we are happy that he did not come to Fiorentina.
"He did not deserve our city and our shirt and the values it represents."
