The referee "shall be the sole judge as to whether all balls offered for play comply with these specifications" and the balls "remain under the supervision of the Referee until they are delivered to the ball attendant just prior to the start of the game," according to Rule 2, Section 1.
A person with intimate knowledge of the process told USA TODAY Sports the ball attendant is a uniformed official – generally the same person each week at a given stadium – who comes to the locker room to pick up the balls and takes them to the officials' locker room for testing.
The ball attendant delivers the balls to the ball boys – usually four provided by the home team and two traveling with the visiting team – who make sure their quarterback's preferred balls get into the game, said the person, who spoke on condition of anonymity because they weren't authorized to speak publicly.
At halftime, the balls return to the officials' locker room, the person said. So, if proper protocol is followed, the only opportunity to manipulate the balls is minutes before kickoff or during the game on the sideline, where there's a risk of anyone in the stadium and dozens of TV cameras seeing it.