The league's involvement represents a significant escalation in the controversy engulfing Carlton, with the AFL now examining the events that led to both players requiring medical treatment in the early hours of Sunday morning. Cowan was taken to hospital via ambulance.
Blues football boss Chris Davies confirmed the development on Wednesday evening as the AFL trade period drew to a close.
"It's an AFL discussion at the moment and we'll leave it there," Davies said. "The AFL are going through a process right now and ultimately, we'll work with the AFL to get to the end of that."
"We've been having discussions with the AFL over the last two or three days, clearly, to make sure that we are at the bottom of that." Asked about the health of the two players, Davies said: "That's the most important thing. They're OK now, a little bit embarrassed, I guess, to put the club in this position."
Davies also confirmed another player had been present on Saturday night, "but not in the same situation". The club had previously said it would investigate the incidents and pass its results to the AFL. It has not disclosed what led to the hospitalisations.