Manning called Vanderjagt an "idiot" on several occasions during a televised interview Sunday during the Pro Bowl.
"Here we are," Manning told Lynn Swann on the sideline. "I'm out at my third Pro Bowl, I'm about to go in and throw a touchdown to Jerry Rice, we're honoring the Hall of Fame, and we're talking about our idiot kicker who got liquored up and ran his mouth off."
Manning said he would deal with the situation when he got back to Indianapolis. Vanderjagt criticized both Manning and coach Tony Dungy last week during a televised interview in Canada.
"I'm not a real big Colts fan right now, unfortunately. I just don't see us getting better," Vanderjagt started before questioning his coach's and Manning's passion.
"Coach Dungy, he's just a mild-mannered guy. He doesn't get too excited, he doesn't get too down and I don't think that works, either. ... I think you need a motivator, I think you need a guy that is going to get in somebody's face when they're not performing well enough."
Vanderjagt has since apologized for his comments. But Manning's "liquored up" comment is a new development.
Manning was clearly disturbed during the first-half interview during ABC's telecast of the Pro Bowl. He called Vanderjagt an "idiot" at least four times.
Vanderjagt, the most accurate field-goal kicker in NFL history, signed a $7.75 million, five-year contract extension with the Colts in November 2000 -- at the time making him the league's highest-paid kicker.
"The sad thing is, he's a good kicker," Manning said. "He's a good kicker, but he's an idiot."
The Associated Press contributed to this report.