"I am sorry again. It is very sad news today for all Americans. I am very, very mad. If I did know one per cent that he is committing such a crime, my son, I would address it myself. I would have called the FBI. I would have called local law enforcement," Seddique Mir Mateen told reporters.
Seddique's son Omar, who carried an assault rifle and a pistol into the gay club in Orlando in the wee hours on Sunday and killed 50 people while injuring 53 others, was later shot dead by the police.
Seddique has been a political activist and the most recent video on his YouTube channel shows him declaring his candidacy for the Afghan presidency.
Both father and son lived separately in Orlando.
"I don't know why he did what he did. I wasn't aware of it. And I always paid attention that he should get higher education and serve the United States of America. And I thank you all for coming in here. And I am very sorry and I am very upset that he did what he did inside the United States," he said.
Meanwhile, the US State Department refuted reports that its officials had met Seddique.
"We have no record of any meetings between State Department policy officials and Seddique Mateen," State Department Deputy Spokesman Mark Toner told PTI.
However, the State Department is aware of reports from social media purporting to show Seddique meeting with State Department officials, he said.
"While we continue to review our records, at this time, we believe he was photographed outside of the State Department's office on Capitol Hill (where we work on consular issues for Members and their constituents)," Toner said, referring to the pictures being circulated on the social media.
Seddique said his family is completely shocked by the terrorist act of his son.
"We can't believe what did he do. And I want to take this message out. I don't allow nobody to do any kind of crime or terrorist act inside the United States. And I don't allow it," he said.
"My principle as a father, my principle as a US citizen, I am against -- I've been, throughout my life, against terrorism, against injustice, against what anyone can do against US, especially my homeland, the US," he told reporters in response to a question.
Seddique said he has no idea why his son took such a action of killing people.