Hopper Jack, the Oscar winner's second child with estranged wife Robin Wright Penn, was recently taken into custody by the Los Angeles County Sheriff's department, reports RadarOnline.com.
Further details about the 16 year old's arrest at his high school in Malibu, California have not been released as the boy is a minor.
The youngster's problems come at a difficult time for the Penn family - the stars are currently going through a divorce after numerous failed attempts to save their 13-year on/off marriage.
A representative for Penn had yet to respond to requests for a comment as WENN went to press.