Immigration Minister Jason Kenney revealed the flag Wednesday, along with one created for William's father, Prince Charles.
William and his wife Kate arrive in Ottawa Thursday for their first royal tour since their April 29 wedding.
The flags, which William and Charles will use when they are in this country, were created by the Canadian Heraldic Authority and approved by Queen Elizabeth.
"These new flags created for the Prince of Wales and the Duke of Cambridge are magnificent expressions of our constitutional monarchy and heritage," Gov. Gen. David Johnston said in a statement.
"As we prepare to welcome Their Royal Highnesses to experience this marvellous country, I am sure that many Canadians will take great interest in these new emblems. As head of the Canadian Heraldic Authority, I am delighted with the work of our Canadian heralds in preparing these designs."
The designs are based on the Queen's own personal flag for use in Canada, using a banner of the Royal Arms of Canada as the basis for the design, the Governor General's office said in the statement.
The flag will be raised during the official welcoming ceremony for William and Kate at Rideau Hall on Thursday afternoon. William's personal flag will be flown day and night at any building where he stays and on all vehicles in which he travels.
But Canadians may not see that much of it, because as the Queen's representative in Canada, the Governor General's flag takes precedence over William's. Johnston will accompany the royal couple on much of their visit.
That means, for example, it will be the Governor General's flag that flies on Parliament Hill's Peace Tower on Canada Day.
Kenney says the government expects robust crowds to welcome the couple. He's hosting a ceremony Friday, where a group of new Canadians will take their oath of citizenship in front of William and Kate, he said.
"They were elated. I think they were from seven or eight different countries and they were thrilled," he said, pointing to one woman who said she's watched the royal wedding several times and is practising her curtsy.
"I think they understand this is their Royal Family upon becoming Canadians," Kenney said.
"Generally, I find a high degree of respect for the Canadian Crown as a central institution of our constitutional monarchy, our parliamentary democracy."
The Canadian Heraldic Authority at Rideau Hall, or Government House, in Ottawa, worked in co-operation with Buckingham Palace officials to design the flags, the first ones created for members of the Royal Family since 1962, when the Queen adopted a personal flag for her own use in Canada.
The flag's background images are the arms of Canada, to which the Queen added a roundel with her cipher.
William's flag includes a wreath of golden maple leaves, representing Canada, and shells from his coat of arms, around a blue roundel that bears a cursive "W" with a coronet above, signalling William is the child of the heir to the throne. The Queen gave William his "W" royal cipher in 2009.
Another red shell from his coat of arms appears in a three-point white label across the top of the flag. The white label, which also appears on the Prince of Wales's flag, is the traditional heraldic mark of an eldest male child.
On Thursday, the public is invited to the grounds of Rideau Hall, the official residence of the Governor General, for the official kick off of the royal visit, Johnston's statement said.
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