Mario Gobbi said the protest turned violent and fans grabbed the striker by his neck. He said other club employees also were attacked during Saturday's confrontation after about 100 fans broke into the training centre demanding to talk to players and coaches. They were not seriously injured.
The training centre in Sao Paulo will be used by Iran's national team during the World Cup in a few months. Corinthians' stadium, the Itaquerao, will host the tournament's opener between Brazil and Croatia on June 12.
Gobbi confirmed to Radio Jovem Pan on Sunday that Guerrero was attacked.
"They tried to strangle the player who scored the most important goal in team history, we didn't deserve this," he said.
Guerrero scored the winner against Chelsea in the Club World Cup final in 2012.
In a statement posted on its website Corinthians repudiated the "act of vandalism" at the training centre and said it tried to postpone Sunday's match against Ponte Preta in the Sao Paulo state championship to "preserve and protect everyone."
It said the players didn't want to play but the match would go on because "several commitments" had already been made with television rights holders and the local football federation.
"Despite the threat and despite the lack of ideal conditions, Corinthians will play in respect to the club and its fans," it said in its statement.
Corinthians lost 2-1 to Ponte Preta, extending its winless streak to three matches and increasing criticism from fans.
"I can't deny that our preparation for this match wasn't what it should've been," Corinthians coach Mano Menezes said. "But we can't use that as an excuse."
Gobbi said the club has already contacted police and will help authorities arrest those responsible for the attack. Security cameras at the training centre would be handed over to investigators, he said.
"This is a case for the police to handle," Gobbi said. "Our employees don't feel safe anymore."
The fans cut through a wire mesh fence to try to reach Corinthians players getting ready to train.
Local media said their main targets were striker Emerson Sheik and former AC Milan forward Alexandre Pato, who was the team's most expensive signing last year but was not a regular starter. Menezes, who replaced Tite late last year, also was among those criticized.
The fans left the training centre after a brief meeting with Menezes. They stayed inside the club for about two hours, Gobbi said.
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