The removal of swathes of the grass followed complaints by some players who had posted videos on social media to demonstrate.
World number two Rory McIlroy and 2015 US Open champion Jordan Spieth have both criticised the decision to chop away dense fescue grass bordering the fairways at Erin Hills in Wisconsin, venue for the tournament which tees off Thursday.
The removal of swathes of the grass followed complaints by some players who had posted videos on social media to demonstrate that the grass was unplayable.
However United States Golf Association chief executive Mike Davis said Wednesday the decision to mow down down the rough was unrelated to feedback from the players and was made in response to heavy rain lashing the course.
"It's not as if we don't listen to feedback from players," Davis told reporters. "But I will tell you in this case, it had nothing to do, absolutely zero to do with what the players were saying.
"We looked at some spots and we said this is simply not going to play properly."
Davis said the decision had been taken in consultation with the Erin Hills chief groundsman, Zach Reineking, who had warned on Monday that further rain at the course could make the fescue unplayable. With a storm dumping two inches of rain on the course late Monday, Davis ordered the mowers into action.
"We all decided Monday afternoon that if it rained that hard and (the grass) laid down we were going to take care of it and mow it down, and get to four or five inches like the mown rough," Davis said. "That's exactly what we did."
McIlroy on Monday had voiced dismay at the decision, insisting that players who were unable to make the fairway shouldn't bother turning up to a tournament often described as the toughest test in golf.
"Really? We have 60 yards from left line to right line on the fairway," McIlroy said when informed of the decision.
"You've got 156 of the best players in the world here, if we can't hit it within that avenue, you might as well pack your bags and go home."