Aubameyang was left out Dortmund's squad for the stalemate against Wolfsburg on January 14 after missing a team meeting, while he did not travel with his team-mates for last Friday's draw with Hertha Berlin.
Dortmund claimed a bid for the 28-year-old had been received from Arsenal at the weekend, though Goal understands the Bundesliga club are interested in Olivier Giroud as a makeweight in the deal.
It is a familiar situation for Dortmund, who saw Ousmane Dembele go on strike before sealing a switch to Barcelona in August, but one Kovac cannot abide.
"It's unreal that clubs and coaches are now at the mercy of the professionals," the Frankfurt boss told Kicker.
"You can't approve of something like that. Where does that end? In anarchy. Everyone can do what he wants, players will come to training when and how they want.
"In my day it was not like this.
"A five-year contract [now] counts as little as a half-year contract. That is very questionable."
The Gabon international is currently the second top goalscorer in the Bundesliga so far this season, netting 13 goals in 15 appearances for Dortmund.
Aubameyang - who was also the Bundesliga top goalscorer with 31 strikes last term - could play alongside former Dortmund team-mate Henrikh Mkhitaryan, should he move to Arsenal.
Arsene Wenger's side are on the verge of landing Mkhitaryan from Manchester United, with Alexis Sanchez set to go the other way, as both players chase work permits.