"The doctors and the trainers have decided to give him a cortisone shot to kind of take away some of that inflammation that's been happening," Ballard said.
"He'll continue to rehab. We're just going to shut down the throwing right now to get this thing calmed back down."
Luck, who had shoulder surgery in January, practiced for two days two weeks ago and then amped up his workload during his two days of practice last week.
"I've watched every session of him throwing, and it's been going really well," Ballard said. "His velocity is good, his motion is good, all that is coming along at a good rate. It's the soreness right now that we're dealing with and have to get through.
"Understand this: Every player is different. Every rehab is different. Every surgery is different. That's why we never put a timeline on this. Every guy is different. The good news is, Andrew is very in-tuned with his body and he's being honest about what's going on. That's what we want and what we need.
"We want to get to a point where he can practice every day. His long-term success is at what we're looking for."
Ballard would not put a date on when Luck will resume practicing. He also didn't shut the door on the possibility of putting his franchise quarterback on injured reserve, which would officially end his season.
"No, not at this time," Ballard said about Luck potentially going on IR.
Wednesday's news is the latest twist in two-plus years of ongoing issues with Luck's shoulder. He originally injured it in Week 3 of the 2015 season, then aggravated it in Week 2 of 2016 and spent at least one day a week on the injury report the rest of the season. He missed all of the team's offseason workouts, training camp and preseason games.
Luck said last week that he thought the finish line was in sight with his rehab.
"It's natural it's going to be some pain and soreness when you're rehabbing an injury," Ballard said. "It's kind of been coming along the whole time. It's one thing that hasn't gone away. We're going to try to shut him and calm it down right now."
The Colts (2-4) will host the Jacksonville Jaguars on Sunday afternoon.