Goncalves, who left Tynecastle in the January transfer window, told the Edinburgh Evening News on Wednesday that he had left the club due to alleged racial abuse from the stands.
Hearts responded with a forceful statement promising to ban any fans found guilty, and Levein has now admitted the problem may run deeper following discussions with the rest of his squad.
Levein said: “Not to this extent, but there have been issues. I don’t want to go into other details, but I have spoken to other players regarding what had happened.”
The Jambos boss echoed the club statement made on Wednesday which promised to ban guilty parties, and insists they will come down hard on anybody who partakes in such abuse.
“I will never experience this so it’s difficult to talk about it, all I can do is provide support and try to help if a situation arises,” he said.
“The club will be really strong on anyone who gets reported for this type of behaviour, I don’t care how long they have been Hearts supporters, if they are found to be dishing out racial abuse to anybody in the stadium, they are gone.”
He added: “As a club we have been very supportive of players with other problems, and I assure you that if Isma had made it known, we would have dealt with this as soon as possible.”