Seven-time European champions Milan have run up losses of €255 million ($300 million) in the last three seasons, way above the €30 million permitted by the rules that are designed to stop clubs from over-spending.
"After careful examination of all the documentation and explanations provided, the Chamber decided not to conclude a voluntary agreement with AC Milan," a UEFA statement said.
The key concerns focus on the takeover of the club by Chinese businessman Li Yonghong.
UEFA said: "There are still uncertainties in relation to the refinancing of the loans to be paid back in October 2018 and the financial guarantees provided by the main shareholder."