Zaki has been reportedly linked with a possible return to the Premiership and the Egypt striker implied that he hopes for another spell with the Latics.
The arrival of new coach Roberto Martinez instead of Steve Bruce also stirred the speculation, but it is now clear that Wigan have closed the door on the Zak.
"I don't think there is any way he could come back," Wigan chief Whelan told the Evening Post.
"Zaki is difficult to control, and you can't have indiscipline like he showed here in your club. There is nothing in it at all.
Indiscipline
Whelan reiterated that Zaki's reckless acts prompted the club not to extend his loan contract, despite a dazzling start in England.
"I didn't even shake hands with him at the end, he just disappeared," he said.
"When you get players with indiscipline like him, you have just got to wipe your hands of them. It's all over with Zaki – full stop."
After hitting ten Premiership goals last year, Zaki turned into an enemy of the state at Wigan, thanks to his repetitive failure to show up on time after international duty.
The Zamalek star is currently taking part of his team's pre-season camp in Switzerland, but is expected to leave for Europe this summer.
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