Zaki, who is on a season-long loan from Zamalek, joined the Latics after a series of bizarre events, instigated by the Whites' initial reluctance to sell him.
However, Whelan believes that Wigan should have no problems keeping their top marksman as he implied that the deal could be concluded in Januray.
"We have got the right to buy him and are not worried about the situation. There is a deal in place," the Wigan chairman told the Daily Star.
"We can do a deal in January. Steve Bruce is a shrewd manager. If he does a deal, all the fine points are sorted out. There are no loose ends."
Next Shearer
Whelan heaped praise upon the Egyptian striker, comparing him to former England ace Alan Shearer.
"The fans love him and as far as I'm concerned he is Alan Shearer the second," he added.
"He is built like him. He has the same attributes and he knows where the goal is.
"When you watched Alan play he was always in the right place at the right time and this lad is the same.
"You just seem to know that he will score. He is powerful and he can smash them in. he is a very clever player."
"Whether that generates interest from big clubs I don't know. But it's a nice problem to have."