Brady said a team official informed him of Lewis' remarks.
"Everyone has an opinion. I think Ray is a great player. He's a first-ballot Hall of Famer. I was fortunate enough to play against him."
Lewis made his comments Monday on SiriusXM Mad Dog Radio after he was asked about the fourth-quarter reception by Dallas Cowboys receiver Dez Bryant against the Green Bay Packers on Sunday that was overturned on appeal because he didn't complete the process of the catch as he went to the ground.
That led Lewis to discuss his disagreement with rules such as defenseless receivers and the tuck rule that, in his opinion, the NFL should never have adopted.
"There are so many rules in this game that is a very simple game. My argument: If you want to make this game and keep this game pure so where integrity drives this game, leave all these man-made lawyer rules out of the game," he said.
NFL owners rescinded the tuck rule in 2013, but Lewis said Brady owes his fame to the fact it existed in 2001 when what seemed to be a fumble by the quarterback on a sack by the Oakland Raiders' Charles Woodson was later ruled to be an incomplete pass after a replay review.
"The only reason we know who Tom Brady is, [it's] because of the tuck rule. There's no such thing as the tuck rule! If the ball is in your hand, and I knock it out of your hand -- whether it's going backwards, forwards, lateral, sideways, however it's coming out -- that's a freaking fumble," Lewis said. "But guess what we created? We created a freaking tuck rule!
"They don't go to that championship game if that ball is not called a tuck," he said. "That's a fumble. ... So now you've got to ask yourself, When did the legacy really start?"
Lewis sought to clarify his remarks later on Thursday as not Brady-centric. In several Twitter posts he wrote:
"I was trying to express my frustration about the Tuck Rule itself. Rules like that should not be part of the game. They lead to controversial plays that impact the outcome of games and that's what everyone remembers, especially when you are talking about playoff games. I have immense respect for Tom Brady and everything he has achieved in this league. He will go down as one of the all-time greats."
On Monday, Lewis, who called himself a "football historian," said he wouldn't allow these rules in the NFL if he were in charge.
"There's a bunch of rules in our game that does not belong in our game. If I'm the commissioner, I leave the game alone," he said. "I tell the people, don't bring me no rules that don't make sense in my game."
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