"It takes time for it to work," Duffy said. "It's only been 48-72 hours. I can see why they [put me on the DL] -- it makes more sense to have a functioning arm here."
That functioning arm belongs to rookie left-hander Brandon Finnegan, who was called up from Triple-A Omaha. Finnegan pitched three scoreless innings after Jeremy Guthrie exited in the second inning of Monday's 14-1 loss to the Yankees.
Finnegan, though, headed back to Omaha to make room for left-hander Jason Vargas to be activated from the disabled list. Vargas, who had a left flexor strain, will start in place of Duffy on Tuesday night.
"[Finnegan] is just protection," Royals manager Ned Yost said. "No point in activating Vargy today. It makes more sense to have someone we can use if we have to."
The Royals also sent outfielder Alex Rios (fractured left hand) on a rehab assignment to Omaha. Yost indicated there was a chance that Rios could rejoin the team this weekend in Chicago, where the Royals play the Cubs.
Duffy was with the team Monday, and he said he plans to throw a side session on Tuesday.
"I'm not panicking or anything," Duffy said. "I know exactly what [the injury] is."
Duffy went through the same type of shoulder soreness last season, he said. That injury heightened when he made a September start at Yankee Stadium and lasted just one pitch.
"That had been building up for about six weeks last year," he said. "I didn't say anything about it. This time, I'd rather nip it in the bud here. We got a lot of the season left."
Jeffrey Flanagan is a reporter for MLB.com. Follow him on Twitter at @FlannyMLB. This story was not subject to the approval of Major League Baseball or its clubs.