The children missed 28 days from last September – more than a third of the school term.
Apart from the illnesses, the Dublin mother alleged that one of the children was bullied.
But a judge sentenced her to 28 days in prison after being told there was no medical evidence of their illnesses or a bullying complaint.
Activating a previous suspended sentence for keeping her children at home, Judge David McHugh said her household was "chaotic".
A warrant was also issued for the arrest of her husband when he failed to appear in Blanchardstown District Court to answer similar charges.
The accused, who cannot be named, admitted failing to ensure her children attended school for up to 36pc of the September to December term last year.
Two of the girls are in second and third class in primary school, while the eldest is in secondary school.
The prosecution was brought by the National Education Welfare Board.
Solicitor Orla Farrell told the court the younger girls had missed 27 and 28 days, absence rates of 35pc and 36pc. The eldest child had also missed 28 days.
A defence barrister said: "She would be the first to acknowledge that she has been given a chance by the court and the court will find it difficult not to activate the suspended sentence."
He said the offences stemmed "not from wilful neglect in parenting terms but she is sometimes overly indulgent with her children when they present with illness".
The accused, who is in her 30s, said she was the one at home who got her children "up and going" and brought them to school.
On the days they were absent they were "genuinely sick", she said. One had slapped cheek syndrome for a week and the on-call doctor she saw would not give her a note, she said.
Slapped cheek syndrome is a contagious illness that can include flu-like symptoms as well as a rash on the child's cheeks, chest, stomach, arms, and thighs.
Other absences were due to "colds and flu, the normal childhood sicknesses".
One of the younger girls was being bullied and would go to school late. Her daughter was "upset every single morning" and would not go in to school unless she held her hand.
She had thought that her eldest daughter had only missed 12 days, but found out she was "going in late, missing half the school day".
Ms Farrell said the board had not been notified of any bullying complaint and the absences were not vouched for.
The defendant said she had called the school secretary and there were days when one child was sent home sick from school.
The case painted a "far from satisfactory" picture of school attendance, but the accused was not at the extreme end of the negligence scale, her lawyer said.
"She strikes me as someone who is a bit overly liberal, indulgent and laissez-faire", he said.
Judge McHugh said the board and support services had done everything they could.
He said he had "no hesitation" in sending the mother to prison.