Stokes, who suffered a torn hamstring on the same left leg in August, was to undergo a scan on Monday night or Tuesday morning after hobbling off midway through the afternoon session clutching his leg.
The inspirational 33-year-old is a doubt to bat in the fourth innings of the Test at Seddon Park, where England have been set a nominal target of 658 to win. They were 18-2 at stumps on day three.
Batting coach Marcus Trescothick said it was "tough" for Stokes to accept he was injured again.
"It's the same hamstring as he's had before," he told reporters.
Stokes's 23 overs in New Zealand's first innings was the most he has bowled in a single day in his 110-Test career.
Stokes was bowling his 13th over of the second innings when he pulled up with a grimace, clutching his leg in his follow-through before hobbling to the dressing room. He did not return.
Trescothick said: "He's been going so well and he's been bowling and playing the role that he does, as an all-rounder and captain.
"He's shown signs during the course of this series of getting back to fitness."
Stokes missed the entire three-Test home series against Sri Lanka in August-September and was only deemed fit enough to join the October series in Pakistan for the second Test after tearing his hamstring.
His 66.3 overs in this series is the most he has sent down in a series as captain.
He pulled up with a back problem during the first Test in Christchurch but there had been no doubt about his availability for the two remaining matches.
"We didn't see it coming. You don't see any signs of these things generally, they just happen," Trescothick said.
"He's pretty realistic about these things when they happen. It's always tough at the start when you realise you're injured again.
"He works dramatically well at what he does with his fitness to get into that shape where he can be.
"We just have to look at how we can manage it."
