"Unfortunately it's quite a significant back injury," Kountouris said before play.
Clarke was clearly restricted - there was no trademark fancy footwork and he limited his shot selection to minimise twisting at the crease. The 33-year-old grimaced regularly, but India failed to make the most of overcast conditions after Australia resumed day two at 6-354.
Clarke's running between the wickets was understandably slow, but he and Smith kept the scoreboard ticking over in the morning session with a handful of sweetly-timed boundaries.
Clarke has three degenerative discs in his lower back and every shot caused a clear pang.
"He's showing a lot of courage ... he's hurting," Shane Warne said while calling the game for the Nine Network. "Some (strokes) are going to hurt a lot more than others, but he's in a lot of pain."
The skipper overcame a recurring left hamstring injury to play the rescheduled first Test. But Kountouris believed his current woes were unrelated to the hamstring issue.
"This is his right lower back. This is his old injury, what he's had in the past," he said. "I don't think it's directly related to his hamstring, because it's the other side.
"We believe it's related to his old disc injuries. With that comes a lot of muscle spasms and other things that cause pain."
Rain delayed the start of play by 10 minutes on Wednesday, while the umpires called for the covers at 11.26am local time before changing their mind. Soon after they had no choice as heavy rain started to soak the pitch. Umpires snuck in 11 balls after lunch before calling for the groundsmen again.
-AAP