The rules were challenged by agent Daniel Striani but his complaints that it affects wages and locks down power for the continent's biggest teams were rejected
The regulations, which have been in place for four years, aim to improve the overall financial health of European football by encouraging clubs to run in a more economically sustainable manner.
While Malaga was the highest profile club banned from European football last season, bigger outfits have felt the pinch recently, with Manchester City and Paris Saint-Germain just two of the teams sanctioned this term.
Last year, agent Daniel Striani challenged the rules, arguing that they would result in restricted investment in clubs and damage player wages while ensuring power in football remained with the continent's biggest clubs.
The Commission, though, sent a letter to Striani and Uefa, rejecting the complaint and insisting it will not investigate it any further.
It was noted that no club had complained to the European Commission about FFP and that the Commission itself was widely consulted about the rules before they were implemented.
Striani has four weeks to submit observations before the decision is made final.
A spokesman said: "Uefa is very pleased that this decision by the European Commission upholds all aspects of the FFP regulations."
The decision comes just days after Uefa laid down sanctions against several clubs, including City, who were judged to have breached FFP rules. The Premier League champions were given a €60m fine to be paid over three years and have been restricted to registering 21 players in next season’s Champions League squad, while they must maintain wages at their present level.
Striani's lawyer, Jean-Louis Dupont, also brought the case in a Belgian court, so it is yet possible it will proceed. He could not be reached for comment.