Startled club directors considered calling off Sunday's match against Ponte Preta before declaring that it would go ahead, and said that employees were attacked and robbed during the invasion.
Photographs showed the fans, many of them shirtless and some hooded, forcing their way into the training ground in Sao Paulo after making a hole in the fence, just as the team were about to start a practice session.
Brazilian media reported that the players fled to their dressing room and locked themselves in before police reinforcements arrived and negotiated with the supporters for two hours.
Coach Mano Menezes agreed to hold a meeting with five representatives of the supporters.
"The Corinthians directors repudiate and deeply lament the acts of vandalism by a group of supporters at the training ground this morning," the club said in a statement, adding that they would co-operate with police to identify and punish the culprits.
"Shortly after these incidents, and in the face of this truculent invasion, the team momentarily did not feel safe enough to play against Ponte Preta on Sunday.
"However, on being told that the club, and consequently the Corinthians supporters and sponsors could be severely punished, the players, coaching staff and board of directors reached the conclusion that we will take the field tomorrow (Sunday).
"The board of directors repeat that we repudiate this morning's actions, in which people were attacked and threatened, belongings were stolen and the club's property was violated."
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