The 31-year-old, playing in his 100th test match, left the field after just 26 minutes of the All Blacks’ 30-22 victory at Twickenham.
“Its been rumbling away for a while,” coach Steve Hansen told New Zealand media after his side continued their unbeaten season.
“He’s obviously very sore. It’s not ruptured, I wouldn’t think, but we won’t know that until we get some scans.
“It’s disappointing for him again. He’s had a wretched time with injuries.”
The All Blacks complete their season next week against Ireland in Dublin. If they beat Joe Schmidt’s side they will become the first top tier team to go through an entire year unbeaten since rugby went professional in 1995.
Carter has been dogged by a series of niggling injuries over the last few years and made just his sixth appearance for the All Blacks in their 13th test match of the year at Twickenham.
A broken hand kept him out of tests against France in June before a calf injury saw him miss matches against Australia in the southern hemisphere’s Rugby Championship.
Hansen said Carter’s latest injury was not related to a torn Achilles’ tendon he suffered while playing for Perpignan in France in early 2009 as that injury was on his other leg.
Carter, who has been granted the sabbatical by the New Zealand Rugby Union, said earlier this year he had considered playing overseas on a short-term contract but felt the time would be better spent having a total break to sort out his injuries and conditioning.
He is not expected to play again until after next year’s June international series when England visit New Zealand for a three tests.
Hansen added that loosehead prop Tony Woodcock would also miss the Ireland match after he sustained a hamstring injury in the first half against England.