The 77-year-old, who cannot be identified, apologised to those she "mistreated" at Nazareth House homes in Aberdeen and Lasswade, Midlothian, while giving evidence to the Scottish Child Abuse Inquiry.
She worked at the Catholic-run orphanages from 1963 until 1980 and said she could lose her temper "on some occasions", but denied a litany of other allegations made against her.
Colin MacAulay, senior counsel, said: "(One accusation says) you did punch her on the head and body, and strike her with a hair brush. Do you accept that you did that?"
The nun said: "Yes."
Mr MacAulay added: "Do you accept then that you did seize hold of her by her hair and drag her around the corridor?
She said: "Yes."
The same replies came when Mr MacAulay asked if she had ever force-fed a child or pushed a girl to the ground from a swing.
Her admissions were in relation to two children in separate homes.
It was heard a child was forced to eat dolly mixtures as a punishment after sweets had gone missing.
The nun said: "I always had dolly mixtures for the little ones. I went to get them and they were missing.
"I just had a few, there wasn't enough. I said 'you might as well take the rest' and put them into her mouth."
When asked why others had come forward with accusations, which she denied, the nun broke down in tears and said "I don't know".
A statement she submitted to the inquiry said her care for some children at the homes amounted to them being "mistreated".
She said another nun at the Aberdeen orphanage would hit youngsters with a hair brush.
The witness added it was this other nun who was in charge of dealing with children who wet the bed, having denied any involvement in humiliating those who did.
She said: "The children used to say they put the sheets on them but I never saw that. If it was one of sister's punishments, I never intervened.
"It was nasty, I thought it wasn't nice."
Mr MacAulay then asked her if she would describe the treatment as cruel.
She said: "I would now."
The inquiry before Lady Smith in Edinburgh continues.
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