Mitchell Santner will miss the first test against Australia in Wellington through a foot injury.

New Zealand coach Mike Hesson is hopeful Mitchell Santner will miss just the first test against Australia.

The allrounder was ruled out of the opening test in the two-match series against Australia starting in Wellington on Friday with a foot injury.

The left-arm spinner and middle-order batsman has been replaced in the squad by offspinner Mark Craig, who struggled in the three-test series against Australia across the Tasman late last year.

Santner was a late withdrawal from the Black Caps side that won their Chappell-Hadlee Trophy ODI decider in Hamilton on Monday.

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Hesson said the 24-year-old had a bruised right foot.

"If we continue to play him, it could turn in to a far longer injury," Hesson said.

"We're hopeful that he'll be right for the second [test].

"It's unfortunate for Mitch as he's been a key player for us so far this summer. The positive news is that we picked it up early and hopefully Mitch can make a quick recovery."

Santner made his test debut against Australia in Adelaide in the historic day-night pink ball test in November and kept his place for the two tests at home against Sri Lanka in December.

In his three tests, Santner has taken six wickets at an average of 31 and averaged 26 with the bat.

On the flat tracks in Australia, Craig took eight wickets at 64.13 and after legspinner Ish Sodhi starred in the one-day win on Monday, Hesson was asked if Sodhi was seen as a replacement option instead of Craig.

"No. Ish has certainly showed that he's a better white-ball bowler at the moment than he is a red-ball bowler.

"That's certainly something that he's working on and that he'll continue to do," Hesson said.

Left-arm swing bowler Trent Boult also missed Monday's victory through illness but Hesson said there's no doubt he'll be ready for the first test at the Basin Reserve.

"Trent was just sick, he's fine today.

"He had a bit of a fever, so lost a lot of energy."

Fellow red-ball spearhead Tim Southee played a Plunket Shield match for the Northern Knights as he continued his recovery from a a bruised bone in his left foot following the December 31 ODI against Sri Lanka.

"Tim obviously got through the first-class game which was great," Hesson said.

"He's come through well. We'll assess him when we get to Wellington today.

"Tim's a huge part of our attack and if he's fighting fit it'll be great to have him back,"