"Managing players' workloads will be an important part of our summer's plans and this is simply an example of that," general manager national selection Bruce Edgar said of the three players heading home early.
"On the flipside, it gives us a chance to assess and evaluate other players in contention for the Cricket World Cup squad, and allows us to work on some of our contingency plans - such as developing Kane's captaincy experience."
The first of the T20s is in Dubai on Thursday night (NZT).
New Zealand squad: Kane Williamson (c), Martin Guptill, Anton Devcich, Ross Taylor, Tom Latham, Dean Brownlie, Corey Anderson, Luke Ronchi, Jimmy Neesham, Nathan McCullum, Dan Vettori, Kyle Mills, Mitchell McClenaghan, Matt Henry, Adam Milne.