Children were forced to eat their own vomit and bathe in disinfectant at residential care homes run by nuns, the UK's largest public inquiry into institutional child abuse was told on Monday.

During evidence on the behaviour of nuns from the Sisters of Nazareth order at two Catholic church-run children's homes in Derry, the inquiry heard that children were beaten for bedwetting and had soiled sheets placed on their heads to humiliate them.

Nazareth House children's home and St Joseph's Home, Termonbacca, were both run by the Sisters of Nazareth in Derry. Forty-nine ex-residents of the two homes gave evidence about their treatment in written and oral testimony to the historic institutional abuse inquiry sitting at Banbridge courthouse.

A total of 16 church- and state-run orphanages, care homes and other institutions in Northern Ireland are under scrutiny in a public inquiry expected to last until June 2015.

Young people at Sisters of Nazareth properties in Derry were known by numbers rather than their names, and many were allegedly subjected to humiliation, threats and physical abuse, said Christine Smith QC, senior counsel for the inquiry.

Outlining the nature of the allegations, Smith told the inquiry that as well as making children eat vomit when they were ill, nuns used sticks, straps and kettle flexes to beat their young charges. The nuns removed Christmas presents from some children as punishments, Smith said.

She said those who had given testimony also accused the nuns of locking them in cupboards and threatening to transfer them to an adult mental hospital at Muckamore Abbey. in Co Antrim, if they did not conform.

Rather than sending the children to school, the Sisters of Nazareth sent them out to work on farms or in the home's laundry, Smith said. She said allegations also included sexual abuse by older children, visiting priests, employees and in one instance a nun.

A senior member of the order made a submission to the inquiry acknowledging that an individual sister or common staff member, having worked long hours with children from troubled backgrounds, may have lost her temper and acted inappropriately. She accepted there was scope for bullying because they could not keep eyes on all the children.

"The sisters always tried to provide the best care with the staff and resources available to them." She said they had little information to give the inquiry about sexual assaults but were extremely upset about them.

At Nazareth House in 1996, a sexual abuse allegation was raised with police. "Police advised the home in 1997 that a prosecution would not be made," Smith said. In August 1997 a further allegation of abuse against the same person was made by two people. The individual was subsequently dismissed.

The treatment of children in church-run residential homes is a key concern of the investigation, which is chaired by the retired judge Sir Anthony Hart and is considering cases between 1922 – when Northern Ireland was founded – and 1995.

Smith said the nuns who ran the homes in Derry had provided only "haphazard and piecemeal" evidence to the inquiry thus far. She said their apology to the hearing this month was "less than wholehearted and rapid", and their "response on the part of the congregation has caused considerable difficulties to the work of the inquiry".

She added: "The congregation is not the only body whose approach has produced problems. We do appreciate that this is not always avoidable but we hoped that such late delivery could have been avoided, given the difficulties which it causes for the inquiry."

Those allegedly abused at the homes will give evidence later this week.

The inquiry heard evidence that the unionist-dominated Northern Ireland government in the 1950s may have known about the conditions in the Derry homes.

Smith quoted from a 1953 report by Kathleen Forest, an inspector for the government's home affairs department, who wrote: "I find these homes utterly depressing and it appals me to think that these hundreds of children are being reared in bleak lovelessness."

Two weeks ago the Sisters of Nazareth became the first religious order to apologise for the way children were treated in their care. The Catholic order De La Salle Brothers, which also ran a number of children's homes, also apologised and accepted there was abuse in their institutions.

A representatives of Northern Ireland's health and social care board said that if the state had failed in any way, it was sorry.

The inquiry which is expected to cost up to £19m, does not have the power to find anyone guilty of a criminal offence. However, if the tribunal does unearth evidence of any crimes committed, this material can be passed on to the Police Service of Northern Ireland.