"Oh, there's no doubt," Kelly said. "There's no way that an equipment manager in the National Football League is going to do something to the football without the greatest quarterback ever to play knowing."
Kelly said he considers Brady a "good friend," and wondered why the four-time Super Bowl winning quarterback would allegedly consider playing with under-inflated footballs.
"You do something like that, you're going to get caught," Kelly said. "And Tom didn't need to do it...but why?"
Kelly also spoke about Brady's Deflategate involvement to NFL Network on Tuesday, saying he "was a little shocked" with the NFL penalties against Brady and the Patriots.
Brady was suspended for four games last week after an NFL investigation concluded it was "more probable than not" that Brady was "generally aware" of team attendants deflating footballs before the AFC Championship game on Jan. 18. Brady is appealing the suspension.
In addition to Brady's suspension, the Patriots were stripped of their 2016 first-round and 2017 fourth-round draft picks and fined $1 million. Patriots owner Robert Kraft, who has spoken against the integrity of the NFL's probe, said the team will "reluctantly" accept the penalties.