Manning's unbeaten Denver Broncos side are due to face the Colts this Sunday, marking the first time that the quarterback has returned to Lucas Oil Stadium since his 14-year stint in Indianapolis ended last year.
Despite Manning still being regarded as a legend at the Colts, owner Jim Irsay recently revealed that he let the 37-year-old go in order to win more Super Bowls than the one he brought them.
Dungy believes that the comments were intended to rile Manning in the build-up to the game in an attempt to have an impact on his performance.
"Jim is making this personal. I'm surprised. I think that's what he's trying to do. Have him make it such a big game he doesn't perform well. I can't figure any other reason to go this way," Dungy told ESPN.
"Without Peyton, there would be no Lucas Oil Stadium. This team would be playing in L.A. right now. I don't understand Jim saying this."
Manning was voted to 11 Pro Bowls and named the NFL MVP four times during his successful spell with the Colts.