The move comes after a toddler died at a home daycare in Vaughan, north of Toronto, last week.
Education officials have admitted that they failed to follow up on two of three complaints lodged against the daycare.
Ombudsman Andre Marin says he'll probe how the government responds to complaints and concerns related to unlicensed daycares.
The Ministry of Education says it's investigating the facility to see if any charges should be laid under the Day Nurseries Act.
It says it's also reviewing all complaints filed against unlicensed daycares in Ontario in the past year to see if the ministry followed up.
The review should be completed within a week.
The New Democrats asked Marin to launch an investigation last week, saying other children have died in unlicensed daycares, including a toddler who was found at the bottom of a pool in 2010.
Marin said he's directed his special response team to complete the "fact-finding" stage of the investigation within the next three months, "in view of the high level of public interest in proceeding with this case."
Earlier in the day, Premier Kathleen Wynne said she was "horrified" to learn of the two-year-old girl's death.
It's "unacceptable" that complaints against the daycare weren't followed up, she said.
Complaints were made about the number of children at the daycare in October, November and December 2012. But the ministry only investigated the one in November with a visit to the daycare, ordering that it comply with regulations.
According to education officials, the long-standing policy is to visit the site within five business days.
It's not yet known what caused the toddler's death.