Zaki has made a big impact in the Premier League since joining on loan from Egypt club El Zamalek but Bruce said he was running out of patience with the player after he failed to return from a match against Zambia last weekend.
Bruce said it was the fourth time Zaki had not reported back on time from international duty this season.
"I really am at the end of my tether with him," Bruce said in a statement on Wigan's website.
"I just feel that it's time we went public on what a nightmare he has been to deal with because I can honestly say that in all my time in football I have never worked with someone as unprofessional.
"Before this latest incident, Zaki had already been fined considerably more than the average person in Britain earns in a year and he will now face another heavy fine. I have already fined him the maximum allowed but this just seems to have no effect.
"I am now fearful that if I don't take firm action, it will disrupt the rest of my squad, who -- to a man -- behave totally professionally."
Wigan received a fax from the Egypt team doctor claiming Zaki has a hamstring injury.
Zaki briefly topped the scoring charts in the Premier League earlier this season but has not added to his 10 goals since December.
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