The news came the same day Cummins' manager confirmed his star client planned to nominate for the IPL auction.
It could set Cummins up for a A$1 million pay cheque - but also added to fresh fears for his growing body.
"It is a concern because his last two first-class games he played in ... he's picked up an injury in both of them," Kountouris said.
"We gave him the best preparation we thought we could give him but it still didn't go well."
Cummins joins fellow quicks Ryan Harris (hip), Mitchell Johnson (foot surgery), Doug Bollinger (hamstring) and Ben Cutting (side strain) as well as allrounder Shane Watson (hamstring) on Australia's growing injury list.
Asked if the injuries were a result of bowlers' workloads, Kountouris said: "That's the million dollar question.
"We need to know more about it. We're working in a changing landscape.
"The scheduling has changed [compared] to what it was 10 years ago, five years ago, three years ago, even this year.
"All these competitions ... they're all here to stay and we've got to get better at managing that."
Kountouris said he had never seen a fast bowler with Cummins' injury and threw up the possibility of the youngster using a shoe insert upon his return.
But he admitted he was still getting to the bottom of the frustrating injury.
"Is it his foot biomechanics, is it just bad luck, is it the hard wicket, is it the spikes, the shoe?" he said.
Cummins was more upbeat, saying he aimed to play the subsequent one-day and Twenty20 series against India and possibly test cricket this summer.
But his IPL plans have raised eyebrows.
Former skipper Steve Waugh even suggested Cricket Australia should caution him.
"The baggy green is No 1 and everything else slots in underneath that," he said.
"IPL right now should be a fair way down on his radar."
Fellow ex-skipper Ricky Ponting rued the fact Cummins' long awaited union with fellow test sensation James Pattinson had been postponed but said the teenager's health was the priority.
"Young fast bowlers especially have to be looked after," he said.
- AAP