A former Catholic care home resident has alleged a six-year-old boy died after a nun kicked him repeatedly in the head during years of sexual and physical abuse at the home.

David, a pseudonym for the former resident, told an official inquiry into historical sexual abuse in Scotland that nuns and staff oversaw a regime of terror at Smyllum House, a children’s home in Lanark run by the Daughters of Charity of St Vincent de Paul.

It emerged in September that up to 400 boys and girls who had lived at Smyllum, which closed down 1981, had been buried in unmarked mass graves after dying at the home, often from TB, pneumonia and pleurisy, and mostly between 1870 and 1930.

Physical abuse was routine in the home, including beatings, slaps to the head, and verbal abuse for the slightest mistake, David said, as he gave evidence on the first day of oral testimony about abuses at three care homes run by the Daughters of Charity.

One of 23 former residents due to give evidence in person, David said several nuns and female staff at Smyllum sexually abused him and other young boys, inducing the children to have sex with them and handling their genitalia.

David said his six-year-old friend, Sammy Carr, was hospitalised after a nun flew into a rage at him in the early 1960s. She had repeatedly kicked him in the head and upper body until David shielded him from the attack.

He last saw Carr, still aged about six, being taken into an ambulance after 10 days in the Smyllum House sick bay. Wiping tears from his eyes and halting several times to compose himself, David recalled being taken by the same nun to see his friend’s freshly dug grave.

A police investigation earlier this year into David’s allegations confirmed that Carr had died of a brain haemorrhage but there was no evidence in the postmortem linking that to an assault. Medical evidence suggested instead that Carr may have had a fungal brain infection, perhaps brought on by malnutrition.

After being moved to another care home run by the order, St Vincent’s in Newcastle,he and one of his brothers were taken to a staff member’s house where they were both sexually abused by two men. Violence was endemic at St Vincent’s too, David said. In his written testimony to the inquiry, he said it was “just another place run by psychopaths. Most of them were absolutely mad.”

David and Fergie, also a pseudonym, another resident who arrived at Smyllum in 1960 as a baby, said bedwetting, which was endemic for the children there, would result in a cold bath and the ritual humiliation of the soiled sheet being tied around their necks. Failing to eat the meals, particularly fish on Fridays, led to beatings in the dining hall, with children knocked off their feet by the blows. David described those assaults as “normal hidings”.

Fergie said she was assaulted and force-fed regularly at breakfast when she refused to eat the porridge. In later life, David was diagnosed with post-traumatic stress disorder, which left him flying into uncontrollable rages.

Before David’s harrowing testimony to the hearing, a lawyer for the Daughters of Charity, Gregor Rolfe, admitted for the first time that one male lay volunteer in the mid-1970s could have sexually abused two boys whom he took on a holiday.

In a formal statement, a member of staff has said for the first time that this summer she had told a senior nun at Smyllum in the 1970s that Brian Dailey, a care worker from Edinburgh jailed in June this year for years of predatory abuse of children in residential homes, had abused the boys.

The order has no records of her complaint, Rolfe said, and it was not passed to the police. “The order is deeply troubled by each of these failings,” he told Lady Smith, who is chairing the inquiry.

“As Daughters of Charity our values are totally against any form of abuse and thus we offer our most sincere and heartfelt apology to anyone who suffered any form of abuse in our care.”

At earlier hearings, the order had insisted they had seen no evidence or records of abuse at Smyllum or their other homes. The inquiry is due to consider evidence from 36 former residents, including 23 giving their testimony in person.

John Scott QC, a lawyer for the campaign group In Care Abuse Survivors (Incas), had earlier told the inquiry that in public, Smyllum was lauded as a showpiece residential home while the nuns insisted it was there to provide safety and security for its residents.

For most of the children there, Scott said, “the ‘Smyllum way’ became shorthand for wicked abuse. They knew what to expect if they were to sin, for example, by crying or wetting the bed.

“The ‘Smyllum way’ did not involve only one or two abusers. It did not just last for a short time. It involved many abusers and took place over decades. It seems to have become part of the institutional memory in the place, for abusers and children alike.”

Scott said that the order’s attempts to play down the evidence against it by blaming a lack of records was unacceptable. The order had to be held accountable and to accept its culpability, he told Lady Smith.

One sister had suggested to the inquiry earlier this year that the survivors were complaining to get compensation, Scott said. “This inquiry has seen how much more there is to survivors than any legitimate demand for money. Prevention, acknowledgment, apology and accountability are what drives them,” he told the inquiry.

The hearings into Smyllum and other Catholic care homes will continue into early 2018. The inquiry will report its findings no earlier than October 2019.