Whittingham said he will treat Wynn like several other injured players who are on the verge of returning by keeping them on the sidelines until Monday's practice.
"That gives them a good chunk of time to heal," he said. "To me, that is the most logical thing to do."
Such a plan would mean Wynn will miss Saturday's scrimmage, the last of the Utes' preseason camp.
Wynn, whose career has been hampered by injuries, downplayed the aches he feels in his shoulder.
"It's nothing to worry about or freak out about," he said. "There is no structural damage, it's just a little sore."
Wynn has thrown well in camp, but his backups, especially Travis Wilson and veteran Jon Hays, have thrown well, too, and have closed the gap between themselves and the returning starter.
However, Whittingham said Friday that Wynn remains the starting quarterback.
"It's a competition just like every other position is, and like I said the gap has shrunk, but in a good way," he said. "Jordan has performed well, and the other guys have increased their level of play, which is what you want to see."
Wynn didn't seem too concerned his absence would put his job in danger and said being on the field for the season opener was more important than being there now.
"I know there are guys right behind me, but at the same time I know my body, and I'm not going to come out and throw my shoulder out," he said. "The goal is to be ready for Northern Colorado."
Wynn has undergone three shoulder surgeries two on his left and one on his right since he joined the Utes.
The junior, who received an extra year of eligibility from the NCAA due to all the games he missed, said he feels healthier now than he has since his freshman year despite the current soreness.
"I just have to get through this soreness and get ready for Northern Colorado," he said.
Wynn's insistence that he is healthy despite the sore shoulder is reminiscent of the way he talked last year. Wynn had surgery to repair his right shoulder in December 2010 and consistently said he was fine although his throwing motion wasn't as smooth as it once was.
Only recently has Wynn acknowledged that he didn't realize how much he was hurting. And he is aware that some might question his health now.
"That is part of the deal," he said. "You just take it day by day and regardless, keep my head up and get through it."