The 26-year-old, who scored 46 in England's victory over the Kiwis on Saturday, has jarred his back and missed practice on Monday.
Bowler Jade Dernbach will be fit after injuring his arm during field drills, with Joe Root likely to replace Morgan.
9 Feb: 1st T20 - England won by 40 runs
12 Feb: 2nd T20, Hamilton
15 Feb: 3rd T20, Wellington
17 Feb: 1st ODI, Hamilton
20 Feb: 2nd ODI, Napier
23 Feb: 3rd ODI, Auckland
5 March: 1st Test, Dunedin
13 March: 2nd Test, Wellington
21 March: 3rd Test, Auckland
New Zealand welcome Ian Butler and Grant Elliott back from injury.Morgan is England's highest ranked T20 batsman - the Middlesex man is rated as the ninth-best in the world by the ICC - and he has scored more than 850 runs at an average of 37.3 in his 33 matches.
His absence would be a big loss for England, who dominated the first T20 international - their 214-7 becoming their highest score in the format before captain Stuart Broad took 4-24 as New Zealand finished on 174-9.
The tourists can ensure victory in the three-match series if they can win in Hamilton, and Yorkshire batsman Jonny Bairstow, who scored 38 from just 22 balls in Auckland, is hoping to continue the momentum.
"To spend some time in the middle was really pleasing and I was pleased with the way I struck the ball," said the 23-year-old, who helped Morgan put on 81 in seven overs at Eden Park.
"We were really pleased with the performance we put in. Everyone contributed, in all three disciplines."
New Zealand were outclassed in the first match and middle-order batsman Colin Munro accepts they got their tactics wrong.
"Obviously Saturday was disappointing - we weren't up to scratch," Munro said. "We had plans to drop the ball a little bit shorter and let them hit to the bigger boundary, but we were quite full and floaty - so we played into England's hands to hit the short, straight boundaries.
"Our lengths weren't right and dropping five catches didn't help. That's not going to happen again."
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