Rossoneri technical director Maldini last month said the Croatia midfielder would be "perfect" at San Siro but the deal would not happen.
Following further speculation, Milan's chief football officer Boban reiterated the point.
"Twenty days ago, Paolo Maldini declared that Luka Modric will not be a Milan player," he told La Gazzetta dello Sport.
"But since we continue to talk about it and write about it without any basis, I would like to repeat that the best player in the world of last year will not be our player.
"As far as I can see, he will still be in Madrid. Obviously, it would be great to have him, but this is the only truth."
Images have previously circulated of a young Modric in Milan colours, and Boban added: "Luka is a person and a player of the highest level.
"We thank him for his good wishes for next season and we are pleased that he has liked our club since he was a child, but it is right to clarify things – out of respect for our fans, too."
While the English transfer window has now closed, the deadline for Italian clubs isn't until August 23, so Milan have plenty of time to wrap up whatever details they are still targeting.
Their first home game comes against Real Valladolid the week after.