"We're not going to adopt a long-gun registry here in Ontario," McGuinty said after touring a local website development company.
"But we will maintain a practice that's been in place since 1978."
Federal Public Safety Minister Vic Toews sent a letter Tuesday to all provincial chief firearms officers, telling them the collection of point-of-sale data is no longer authorized under the Firearms Act.
He asked the RCMP to notify him "immediately" if they learn that chief firearms officers are engaged in "unauthorized data collection."
But Ontario has a different interpretation of the Firearms Act, and it will be up to the federal government to introduce legislation to counter the practice, said McGuinty.
"Let's not have an exchange between the RCMP expert in this area and the provincial experts in this area," he said.
"Let's turn it back to the feds and say if your intention was to not only eliminate the long-gun registry but a pre-existing practice, I think you need to make that clear.
"Right now there's obviously some uncertainty."
Ontario Community Safety Minister Madeleine Meilleur has written Toews to clarify the province's position on the issue.
Meilleur says recent media attention created confusion, so she wanted Ottawa to know Ontario does not want a provincial gun registry and will "comply fully" with the requirements of Bill C-19, which killed the federal long-gun registry.
But in an interview, Meilleur said Ontario retailers will continue to take down names and address of anyone purchasing a gun as part of the permit process.
She said the chief firearms officer of the Ontario Provincial Police interprets section 58 of the Firearms Act as giving him the power to impose that requirement.
Quebec has mounted a legal challenge preventing the destruction of federal long-gun registry records.
Conservative MP Candice Hoeppner, Toews' parliamentary secretary, suggested in the House of Commons on Friday that Ontario was contravening the intentions of the federal government by continuing to collect gun owner data.
"Bill C-19 should be complied with, the spirit and the letter of the law, and the minister directed CFOs throughout the provinces and the RCMP to comply with that," she said.
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