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The paceman will join the Black Caps in Hamilton in preparation for the second test against England.
With Trent Boult injured, Ferguson and Matt Henry will jostle for starting spots alongside fellow seamers Tim Southee and Neil Wagner.
Ferguson will be replaced in the Auckland side by Matt McEwen.
It is a small relief for Otago. But Auckland still features a classy line-up including Colin Munro and Martin Guptill.
The pair put on 155 for the first wicket on Monday, so the Volts attack will be tested.
A decision on whether experienced opener Hamish Rutherford plays will not be made until this morning.
He has been sidelined since being struck by England speedster Jofra Archer while playing for New Zealand A earlier this month.
Ferguson’s absence removes a significant threat for Rutherford, who missed a significant part of the season in 2016-17 through concussion.
All-rounder Josh Finnie dislocated his shoulder while fielding during the 117-run loss to Canterbury on Monday and has been ruled out for today’s match.
‘‘We will see how he goes for [Friday’s game against Wellington] but we won’t take any unnecessary risks,’’ Otago coach Rob Walter said.
Opener Camden Hawkins is on standby for Rutherford.
Otago started the one-day tournament with a nice win against Northern Districts. But back-to-back losses have left the side in fifth place.
It badly needs a win today or on Friday to stay in touch with the top three.
It is the batting which needs to lift the most. Other than Nick Kelly, the top order has struggled.
Walter described the loss to Canterbury as ‘‘one of our poorest performances for a while’’.
‘‘Obviously we have missed Hamish and hopefully he will be back. If he becomes available that will create a change in the top order.’’
Wicketkeeper Mitchell Renwick will drop down the order should Rutherford play.