The Egypt striker has heavily impressed since joining the Latics from Zamalek on a season long-loan.
Zaki netted five goals in his opening seven Premiership games to become a fans' favorite at the JJB Stadium.
Bruce is worried Wigan might face competition to keep hold of the combative frontman.
"It's a double-edged sword – the better he does here, the more expensive he will be," the English manager told Wigan Evening Post.
However, Bruce remains confident Wigan will be in pole position to sign Zaki on a permanent basis when his loan spell ends.
"Zaki is ours at the moment – let's enjoy while we can. We will try to set up a deal when the time is right."
"We're in pole position to sign the lad because he's here at the moment."
Surpassed Expectations
Bruce admitted he didn't expect that Zaki would make such an impact in the elite competition.
"I've got to say Zaki has started better than we thought he would."
“We brought him here because we thought he could make an impact, and we're delighted because he's certainly done that.
"There's a long way to go yet, a long winter ahead. Hopefully he'll continue how he has been doing."
Zaki is expected to take part in Egypt's World Cup qualifier against Djibouti on Sunday after shrugging off a calf injury.