The former Inter Milan player has been linked with a January return to the San Siro after finding his chances limited at the Etihad Stadium, with a number of high-profile incidents heightening speculation he could soon call time on a two-and-a-half-year spell in Manchester.
But Berlusconi appeared to dispel any thoughts of a potential bid for the 22-year-old last week by calling Balotelli "a rotten apple", a phrase he retracted on Monday night.
Speaking to Sky Italia, he said: "What I said was based on the fact that I feel positive people are useful in the changing room.
"I was not referring to Balotelli and I apologise if it is was taken as a slur against him.
"Could he still come to Milan? No one from my club has held any talks with him, and neither (vice-president Adriano) Galliani or I has identified him as a transfer target."
At last week's Ballon d'Or ceremony, Berlusconi had told reporters: "The name of Balotelli never came into my thoughts, he is a rotten apple and could infect every group where he goes, even Milan."
Milan appeared to be freeing up funds in a bid to capture the Italy international, a self-professed Rossoneri fan, by selling Alexandre Pato and Robinho to Corinthians and Santos respectively.
The former completed a 15million euro move but talks over Robinho's return to Brazil fell through, leaving Milan with four senior strikers and insufficient resources to prise Balotelli away from City for a reported asking price of £25million.
The Serie A club could still move for Empoli defender Riccardo Saponara or World Cup winner Cristian Zaccardo of Parma, though.
When asked whether Milan were likely to bolster their squad before the end of the current transfer window, Berlusconi tried hard to keep his own counsel.
"I hope so," he added. "I am pestering Galliani because there are a few players I would like us to sign, ones we could bring in by the end of January.
"I won't name names, I've been told not to. Galliani told me, 'President, don't name names if you want us to succeed'."