The toddler was found in the toilet of Honey Bees Day Nursery in Birkenhead after her worried parents raised the alarm.
It is not yet known how the girl became unaccounted for and an investigation has been opened by Wirral council.
Staff involved have also been suspended following the incident.
Parents of children who attend the nursery have, unsurprisingly, been left shocked by the incident and blame the council for overstretching its staff.
One parent told The Mirror: ‘Last year they were trying to close the Sure Start nurseries, (and) from my eyes they have been running it down for the last 12 months, not replacing staff who have left, getting in agency staff.’
They added: ‘At times we have not even known the names of the people we have left our [child] with… The staff there have been totally unsupported by the council.’
Wirral’s director of children’s services Julia Hassall said: ‘A thorough investigation is being undertaken into how a child was left unattended within the nursery.’
‘Although the child was not physically harmed in any way, we are taking this incident extremely seriously and took immediate action as soon as it happened.’
‘The staff concerned have been suspended while an investigation takes place, which is a neutral act while we determine any conduct issues that would need to be dealt with through the disciplinary process.’
She continued:‘We have reviewed procedures at the nursery and have addressed staffing levels to prevent any interruption to children’s care during the investigation.’
‘I would like to reassure parents that the safety of children is paramount and we are dealing with this issue as a priority.’