Pte Gavin Williams, 22, of Hengoed, Caerphilly, was made to do intensive exercise as an informal punishment.
Former sergeant Russell Price, one of three cleared of his manslaughter, said physical punishments were "common knowledge" at the time.
He was visibly upset giving video link evidence at Salisbury Coroners' Court.
The inquest was told on Wednesday an "extra system" of punishment operating outside official rules was in place when Pte Williams died in 2006.
He was ordered to carry out intensive exercise for drunken behaviour before collapsing at Lucknow Barrack in Wiltshire.
He suffered heart failure after the "beasting" and ecstasy was found in his blood when he died.
Mr Price, who had been tasked with addressing disciplinary problems within the battalion at the time, said the punishment was used to embarrass and senior officers would overlook it.
He said he did not recall being told to abide by disciplinary rules which stated physical training should not be used as a punishment.
Describing Pte Williams' treatment in the medical centre, Mr Price said: "It was horrible in there sir - I wasn't trained for it.
"One minute he'd be alright, and the next minute he'd be shouting 'get off me'."
But he denied witnessing any ill-treatment of Gavin.
"It was proper restraint, there was nothing clever going on," he said.
He added: "I am truly and deeply sorry for what's happenedâ€¦ it breaks my heart and I am so sorry for the loss of Gavin."
A former sergeant who was cleared of the manslaughter of a soldier who died after a so-called "beasting" has said he is "truly sorry" for what happened.