During Sunday's postgame news conference, Prescott said it was "sad" to see fans throwing things at his teammates as they walked off the field after the NFC wild-card game. However, when he was informed by a reporter that the objects were directed at the officials, he said, "Credit to them then. Credit to them."
Prescott was given an opportunity to walk back the comments at the conclusion of his news conference, but the Pro Bowl quarterback didn't.
On Tuesday, Prescott apologized for his comments with a series of posts on social media.
"I deeply regret the comments I made regarding the officials after the game on Sunday," he wrote on Twitter. "I was caught up in the emotion of a disappointing loss and my words were uncalled for and unfair.
"I hold the NFL officials in the highest regard and have always respected their professionalism and the difficulty of their jobs. The safety of everyone who attends a game or participates on the field of a sporting event is a very serious matter. That was a mistake on my behalf, and I am sorry."
Prescott, who is one of the finalists for the league's Walter Payton Man of the Year Award, received backlash for his comments from media and the National Basketball Referees Association, which encouraged the NFL to take action against Prescott to "discourage this deplorable behavior in the future."