The 26-year-old batsman was ruled out of the remainder of the series when he broke a rib after he was struck a fearful blow from a Glenn McGrath delivery in the opening match at the Melbourne Cricket Ground on Friday.
England said the injury would take between three and five weeks to heal, and are sending the middle order maestro home to recover in time for the World Cup campaign in the Caribbean.
"It's disappointing in a weird way, a sad way because the majority of the team liked watching him bat," Fleming told reporters on Saturday.
"It would have been different playing against him and it's obviously a huge blow for the tournament and England."
The round robin phase of the tournament is widely seen as a question of who will play Australia in the three-match finals next month, and Fleming insisted England were still in the running despite their eight-wicket defeat to the hosts on Friday.
"We're not coming off startling form either. We're not exactly brimming with confidence, but we've got a good understanding of our one-day game.
New Zealand drew their one-day series with Sri Lanka last month, but were skittled for just 73 in the fourth match after the visitors had posted 262 for six.
Fleming believed that after a demoralising tour of Australia which saw England routed 5-0 in the Ashes series, Michael Vaughan's one-day side would relish the challenge of facing new foes in New Zealand.
"If you get a new challenge it's often a breath of fresh air to get your teeth stuck into a new group of players and new coloured uniforms," he said."
"We expect that they'll be desperately looking forward to this and showing to the English public that they're been up against a good side. If they beat us things won't be as bad for them."
New Zealand play their opening match of the series against Australia in Hobart on Sunday before taking on England at the same ground on Tuesday.
