In interviews on two television networks, Scott Johnson defended 13-year- old Mitchell. "My son is not a monster," he said.
Mr Johnson, a lorry driver of Minnesota who is divorced from the boy's mother, offered condolences to the five victims - four girls and a teacher from Westside Middle School.
Mitchell Johnson and Andrew Golden, 11, were charged with murder on Wednesday. Funerals of two of the girls, Paige Ann Herring, 12, and Natalie Brooks, 11, were held yesterday.
Struggling to contain his emotions, Mr Johnson said, "I don't have any explanation for any of this. Nobody does." He said he had seen nothing in the boy's behaviour or state of mind that could have foretold Tuesday's events.
Mr Johnson was driving his lorry in Texas when he heard about the shooting on the radio on Tuesday. He was only reunited with his son at the hearing where the murder charges were read to the boys.
Mr Johnson was allowed a few moments to hug his son. "It's the most difficult thing I've had to do," he said of that meeting. Saying that in those few moments Mitchell had shown remorse, he added: "The truth about my son is that my son is not a monster."
A police chaplain, Rev Jerry Jolly, asked for compassion for the boys' parents, who were devastated by what had happened.
The funerals of the remaining three victims are scheduled to be held this weekend.