According to the Sunday People, Mourinho instead decided to bring in players from the Under-16s squad to perform the duties after "becoming dissatisfied with the previous standard".
United's team of ball boys and ball girls had previously been supplied by the United Foundation but Mourinho made the change in order to provide a "slicker operation" and speed up play.
"The manager wasn't happy with what was on offer before from the ball boys and girls. He wanted a much slicker operation - especially when United are on the attack or time is running out," a source told the newspaper.
"He felt by bringing in lads from the Academy teams - boys who understand the nuances of the game and the urgency of certain occasions, it would help speed up play at crucial moments.
"Of course, people may speculate whether opponents are given the same courtesy if they are on the attack or chasing the game."
Mourinho previously escaped an FA sanction while serving as Chelsea boss in 2014 after he informed a Crystal Palace ball boy that he "could be punched" for slowing down play.