Speaking to CBC Radio's The House, Wynne said she asked Harper to attend the premiers' meeting in Ottawa at the end of this month.
"I did mention to him in our meeting that he would be welcome to come to the meeting," Wynne said. "I think it would be terrific if the prime minister — I've said that all along — it would be great if the prime minister would sit down with the premiers of the country."
In a statement, Harper's spokesperson confirmed the prime minister will not attend, stating he regularly meets one-on-one with his provincial counterparts.
Harper and Wynne had their first meeting in more than a year on Monday, which Wynne later described as a "productive discussion."
Relations between Ontario and the federal government have recently appeared strained over issues including the push for a new provincial pension plan.