The 24-year-old Anderson has not played for Mike Hesson's team since the first test loss at Lord's last month, with the hope the big-hitting left-hander would be able to recover to play some part during the five-match one-day series.
"Corey has been working hard to get back to full fitness for the one day series but he hasn't been able to overcome this injury," Hesson said. "We felt the best course of action was to send him back to New Zealand for further assessment."
Anderson had a MRI scan which revealed a new stress fracture in his back and would need further testing on the injury.
Anderson's absence could cause some issues for New Zealand in the future with fellow all-rounder Jimmy Neesham also unavailable due to a stress fracture in his back.
All-rounders Neesham and Anderson provide balance to Brendon McCullum's team with their batting at number six and operating as a fourth seamer in either tests or one-day internationals.
Anderson has recently filled the role in the limited-overs format, with Neesham preferred in the longer form of the game.
Grant Elliott and rookie left-arm spinner Mitchell Santner have filled the hole in the two games of the enthralling one-day series with England so far.
After being hammered for more than 400 runs in the first match at Edgbaston, New Zealand blasted 398 for five against England in the second game at the Oval with Ross Taylor stroking his 13th one-day international century.
Eoin Morgan's side were positioned to chase it down before rain forced them off when they needed another 54 runs from 37 balls and with Adil Rashid and Liam Plunkett well set at the crease.
When the players returned, the Duckworth/Lewis calculation had made the remaining run chase a virtually impossible 34 runs from 13 balls and New Zealand won by 13 runs as England finished on 365 for nine from 46 overs.
The third match is on Sunday at the Rose Bowl in Southampton and New Zealand were yet to make a decision on whether they would call a replacement for Anderson.
(Reporting by Greg Stutchbury in Wellington; Editing by Sudipto Ganguly)
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