Mpofu was replaced on Tuesday in a 20-man training squad by Tendai Chatara, who is uncapped at Test level.
Zimbabwe face the Black Caps in a one-off Test in Napier starting on January 26, followed by three one-day internationals and two Twenty20 games. New Zealand won the one-off Test, two out of three ODIs and both T20s on their recent tour to Zimbabwe.
Zimbabwe coach Alan Butcher said Mpofu's injury was a blow, but added "we will be underdogs, yes, but we will not be inferior to our opponents."
Butcher also said promising left-arm seamer Brian Vitori was fit again after he missed the home series against New Zealand with a shin problem.