Boult is dealing with an irritated disc, the same niggle that forced Tim Southee off the field during the first Test.
Southee played at the WACA but it was a close thing, the paceman only proving his fitness the day before the second Test started.
NZ coach Mike Hesson says he'll know more on Wednesday about Boult's chances of featuring in the inaugural day-night Test.
If Boult is unable to bowl at full intensity then he won't play the series finale that starts on Friday.
Wagner, called into the squad as cover after the first Test, will almost certainly be promoted to the XI if Boult is ruled out.
The South African expat may lack Boult's profile and late swing but he is a workhorse, fiercely competitive and has pink-ball form.
Wagner claimed five wickets in last weekend's day-night tour match at the WACA.
"For him to come in and bowl the way he did in his first hit-out on tour, it's really pleasing to know he's there and ready to go," Southee told AAP.
Not that Southee was surprised with Wagner's consistency against Western Australia.
"He's shown over a long period of time for us what he's got," he said.
"The job he's done for us over the previous couple of years has been outstanding.
"A lot of the time the hard work he's done has gone unnoticed.
"It was nice to see him get some wickets at the WACA."
Southee is confident he is over the worst of his own back problems.
The right-armer bowled 54 overs in the second Test but noted he only suffered from "general stiffness" in the following days.
"The majority of the bowlers got through a fair chunk of overs," he said.
"Every now and then you have to bowl a few more overs than you thought you would, that's part of your trade. You box on and just do it.
"It was nice knowing we had a couple of days off .. then I got through 10 overs against WA and it [the back] was alright."
