Agnelli insisted that the Coach - who recently extended his contract until 2015 - was not in danger of any punishment.
"The picture that is emerging in the light of the investigation from Cremona is extremely worrying for the world of football," Agnelli said.
"We are all following it with apprehension and bitterness. However, I do not think that Antonio Conte is part of this bleak picture.
"The role attributed to him is insignificant. We know what he has achieved this season and I have personally known him for 20 years - I am aware of his human qualities.
"At this stage it is right to respect those who are investigating, but it is also right to respect the people who have been caught up in this.
"There are things that still need to be verified. The club and I are standing by Conte and Leonardo Bonucci. I hope our defender gets through this and is able to have a splendid European Championship.
"I want to make something very clear before any speculation starts. Antonio Conte is and will be our Coach next season when we return to the Champions League."