Crane, who was unlikely to feature in the series, felt discomfort earlier this week during training in Hamilton. He had initially been named in the squad for the first two-day warm-up match with the pink ball, and as recently as Thursday was bowling on the outfield at Seddon Park, but was sent for two scans which revealed the injury that will rule him out of the start of the domestic season for Hampshire.
"The scan results have shown he has a partial stress fracture of the back, we've caught it relatively early so unfortunately, he's going home," Chris Silverwood, England's bowling coach, said. "Like anybody would be, he's a little bit upset he's going home but that's life and part and parcel of professional sport."
Leach, 26, was the standout performer on a poor tour for the Lions in West Indies, where they were beaten 3-0 in the four-day matches, with 18 wickets in the three matches convincingly out-bowling Crane. He has finally secured his first England call-up having come close in India in late 2016 only to find he needed remedial work on his bowling action.
After working on his action, Leach claimed 51 wickets in Somerset's 2017 County Championship campaign - the best haul by a spinner in the Championship - to take his tally over the last two seasons to 116 wickets, but was overlooked for the Ashes tour as England went for Crane who made his Test debut in Sydney.
Crane claimed 1 for 193 in that match and then struggled on the Lions tour taking just one wicket in the first two four-day matches, in which he sent down just 26.4 overs. Stuart MacGill, the former Australia spinner who has acted as a mentor to Crane, had arrived in New Zealand on Friday to work with England's spinners for a week.
James Anderson, who suffered a serious stress fracture early in his career, offer words of encouragement. "It's tough, especially when you have a chance on a tour like this but it happens unfortunately," he said. "Around that age you are susceptible to those stress injuries but the advice the lads will be giving him is that he's young, has plenty of time on his hands, is a serious talent and if he works hard I'm sure he'll come back strongly."
Until recently England would have had another legspin option to call on but Adil Rashid announced during the limited-overs leg of this tour that he was shelving first-class cricket to focus on the white-ball, although even if he had been available it is unlikely he would have been selected.
Leach will not arrive in New Zealand until early next week and it remains unlikely he will earn a Test debut in this short series unless Moeen Ali is injured.