Liz Sandals announced the investigation after learning that two out of three complaints made against the daycare where the child died were not followed up properly by her ministry.
"This is clearly unacceptable," Sandals said in a statement late Thursday, adding that she was "devastated" to hear about the child's death.
"I have directed my deputy minister (George Zegarac) to conduct a detailed examination of this incident as well as related ministry processes."
The review of the ministry's lack of compliance is expected to take a week to complete, after which time the government will "take appropriate action as necessary."
The toddler died Monday evening at a home daycare that has since been shut down after officials found several health infractions. The child's cause of death has not yet been determined and homicide detectives are investigating, as is customary in cases when a child under the age of five dies.
3 complaints filed in 2012
Sandals said the ministry examined its records after the tragedy to investigate previous complaints that may have been levelled against the facility. They found three that were filed last year — one in October, another in November and a third in December.
However, only the October and December complaints — bringing up concerns regarding the number of children who were being cared for at the centre — were properly followed up by a site visit from ministry officials.
According to reports, there were more than 25 children receiving care at the facility. By law, unlicensed providers can care for only up to five children under the age of 10.
The ministry said that it is "longstanding policy" to follow up complaints with a site visit within five business days. Only the November complaint was found to have been addressed in accordance with this policy.
As police continue to probe the Vaughan incident, the ministry is also investigating whether there will be grounds to lay charges against the daycare under the Day Nurseries Act.
An autopsy on the toddler is scheduled to be performed within the next two weeks.
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