"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."
The defiant statement came as RCMP Commissioner Bob Paulson warned chief firearms officers across the country not to create anything that resembles a long gun registry.
Federal Public Safety Minister Vic Toews sent a letter Tuesday to all provincial CFOs, 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 provincial authorities are engaged in "unauthorized data collection."
That was followed Thursday by a letter from Paulson, instructing CFOs "to ensure that the licensing conditions you impose on business records pursuant to the Firearms Act do not facilitate the creation of long-gun registries in your jurisdictions."
“The coming into force of the Ending the Long-Gun Registry Act leaves no doubt that Parliament has sought to eliminate any form of a long-gun registry,” Paulson wrote.
But Ontario has a different interpretation of the law, and it will be up to the federal government to introduce legislation to put an end to a long-standing 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 addresses 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.