ServiceOntario and its financial sector partners are investigating, and police have been notified.
The news comes as Toronto and Peel Region police are warning about new methods being used to skim debit and credit cards in the Greater Toronto Area.
Minister of Government Services Harinder Takhar says the decision to pull the kiosks from service was made "out of an abundance of caution."
He says he wants to make sure that ServiceOntario's customers continue to be protected.
Customers can still access services at serviceontario.ca or can visit one of nearly 300 ServiceOntario centres in the province.
ServiceOntario provides health card, driver's licenses and vehicle registration services, among others.