He's expected to run in the outfield after taking a knock from a Matt Henry delivery in the first session of the opening day at Lord's.
Anderson's absence leaves New Zealand a pace bowling option short compared to the first test XI, although he only bowled eight overs.
If Watling's knee injury is deemed a liability after assessment overnight, Doug Bracewell, with a similar test bowling average (55 wickets at 35.10 v 58 wickets at 34.48) but higher first-class batting average than Neil Wagner (24.73 v 16.75), would be in line for a call-up.
Both delivered strong spells against Somerset and Worcestershire (Bracewell eight wickets at 27.75, Wagner six wickets at 28.16).
"Both B-J and Corey are doubtful at this stage," captain Brendon McCullum said before the final training session.
New Zealand are undefeated in their last six test series.
McCullum was surprised at reaction in some quarters, which called for them to scale back their aggressive approach.
"Playing this style gives us our greatest opportunity to win the test and the series. We went down [at Lord's] but played some pretty good cricket throughout, it was a credit to England being good enough to run us down. The more we do that, the more we become comfortable with that, although at times we will be beaten.
"When you lose a test, people's thoughts head in a different direction. The first thing they attack is the way we played our cricket, but I make no apologies."
The captain backed his players to wrest back the advantage, provided they can maximise the playing time with rain forecast for four of the five days.
"We've got some good players in the group and to score more than 500 in first innings [at Lord's] is testament to that. It's not a case of panic stations - we need to improve a couple of rough edges. Scoring 743 runs and taking 20 wickets on most occasions are the sort of numbers to win.
"Our plans were fine but we didn't execute them as well as we could have. We've tinkered them slightly. We've got to ask: Was the last performance how they want to play the game, or did they stumble on it?
"Our team is better than any I've been involved with here. To lose hurts a lot, but there's a steely resolve to turn it around."
New Zealand won a test at Headingley in 1983, their first of four in England. Lance Cairns took 10 wickets and Sir Richard Hadlee, in one of just four instances in his 86-test career, took none. In their other tests at the venue New Zealand have lost five and drawn one.
McCullum hoped this match will go some way towards boosting their chances of a return to three-test series.
"We've got to earn the right to that. For so long we've sat in the doldrums and our performances didn't warrant teams playing us in three-test series. We need to get back to a level of respect where teams want to do that. The first test at Lord's was a full house every day, hopefully we keep doing that."
England are expected to field the same XI from the first test.
Captain Alastair Cook said he would be encouraging his players to bat in the same liberal fashion which saw all-rounder Ben Stokes score 193 runs and Joe Root 182 across the test.
"I've always been a fan of encouraging players to play in the same fashion as the reason they got picked."
Cook is poised to become the highest test runs scorer for England in his 114th test. He needs 32 to overtake his Essex mentor Graham Gooch, who made 8900 in 118 tests.
