Prior was sent down after his Cactus League start against the Colorado Rockies in which he gave up three runs, none earned, on two hits and two walks over three innings. A decision had been made before the start; Wade Miller will be the Cubs' fifth starter after a solid spring.
"Obviously, in some ways it wasn't [a] tough [decision], because in the long run, it's the best thing for him, and if it's the best thing for him, it's going to be the best thing for the Cubs," Chicago general manager Jim Hendry said. "He's making progress. I thought, besides the linescore, that he threw the ball better today than he did in Peoria the last time out. Every time, he's been better.
"He's not quite there yet -- I don't think he would disagree with that," Hendry said. "He's a competitor, so he would want to take his turn even if he wasn't all the way back. I think the foundation is being built for him to be all the way back."
Prior, 26, had problems with his right shoulder last season and was limited to nine starts. He spent the winter rehabbing his shoulder, and had been able to keep up with the other pitchers in spring workouts. But his velocity was down and his mechanics were out of whack. On Wednesday, radar guns showed him reaching 87 mph. He finished Spring Training with a 6.97 ERA in four games, giving up 14 hits and nine walks over 10 1/3 innings. He struck out six.
"I told Mark that there's a marked difference from what we're seeing now and what we saw much earlier in the spring," Cubs manager Lou Piniella said. "He's come a good ways. He just needs to continue to work. It wasn't easy [to tell him]. At the same time, this is good for his career."
Piniella had announced Miller as the fifth starter on Tuesday because he didn't want Prior overextending himself in Wednesday's game to try and make the team.
"[Prior] has improved a lot," Piniella said. "He just needs to keep working. I told him if it's another month, another three weeks, we'll know when he's ready and he will, too."
Hendry said the Cubs will have a team official with the Iowa Cubs to monitor Prior's progress.
"We'll make a spot for him when he's ready, I promise you that," Hendry said.
Prior was not available for comment after Wednesday's game.
"I'm sure he's disappointed," Hendry said. "I think he sees it coming that he's getting more successful and getting better. Who wouldn't want to be part of a Major League club when you break? It's awful hard for players to understand that for us, Opening Day is not the telltale. We're only married to the roster we're breaking with for nine days unless somebody's hurt."
The Cubs' No. 1 draft pick in 2001, Prior has a 42-29 career record and 3.51 ERA. He's no stranger to the Iowa Cubs. He made three starts for the team in 2002 before he was promoted to the big leagues on May 22. Since then, he's made three rehab starts for the Iowa team, one each in 2004, '05 and '06.
Prior is healthy, which is why the Cubs did not place him on the disabled list.
"He needs to pitch," Hendry said. "He's healthy and he needs to keep building on what he's done the last couple weeks."
"He's made a lot of improvements," Cubs pitching coach Larry Rothschild said. "We just don't want to retard the progress. Everything's been good and it's all positive. It's just a matter of building more arm strength and letting him get enough innings in and getting him comfortable with what he's doing."
Even though the news was difficult to hear, Rothschild said he felt Prior handled it well.
"I think it would be tough for anybody, but I think he's an intelligent guy and understands what's best for him will ultimately be best for everybody," Rothschild said.
Outfielder Angel Pagan and right-handed pitcher Rocky Cherry also were optioned to Iowa.
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.