The NFL said McKinnie missed practice Friday and Saturday and is subject to a fine. His agent didn't respond to messages seeking comment.
McKinnie released a statement through his publicist Saturday evening, saying he withdrew from the game because of injury.
"I am extremely honored to have been selected for this year's Pro Bowl," McKinnie said in the statement. "However my ongoing injuries in my feet and left ankle that I have encountered during the last portion of the season has hindered me during this week's training and preparing myself both mentally and physically for this Sunday's Pro Bowl game.
"I am very knowledgeable and appreciative of all my loyal fans and supporters and would like to apologize if I may have disappointed you in any way, but getting back 100 percent healthy at this time is my number one concern to perform even better in the upcoming season."
This was the first Pro Bowl selection for McKinnie, whose Vikings lost to New Orleans in the NFC championship last Sunday.
Defensive end Julius Peppers also had an unexcused absence Friday, but was back at practice Saturday.
Since the rosters for Sunday's game in Miami were first announced, more than a dozen players have been scratched.
Information from The Associated Press was used in this report.