When staff did a head-count they discovered they only had 16 children. It was then found the missing boy had let himself out of the basement creche on Herbert Street and the alarm was raised.
Gardai found the boy 250 metres away, in Wilton Place.
The Merrion Montessori and Nursery on Herbert Street has since closed.
The HSE took a case against Sarisha Kelly, who then owned the creche, but she was cleared of negligence.
In dismissing all matters against Ms Kelly, a judge at Blanchardstown District Court said the behaviour of the HSE in the case was "nothing short of disgraceful".
Judge Anthony Halpin said he was satisfied the Montessori took reasonable care of the child and he fully accepted the accused was not conscious or aware a child had been left behind.
He said the minders suffered a momentary loss of concentration, which was bound to happen on occasion, and it was unfortunate that a child was lost sight of.
In his ruling, Judge Halpin said Ms Kelly's employees were subjected to "Gestapo-like interrogation" by the HSE inspectors and fair procedures were disregarded.