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Five wickets from spinner Akila Dananjaya dented the Black Caps' hopes of building an imposing first innings score, a task that looked likely on two occasions before Dananjaya twice claimed a quick flurry of wickets.
Yet, a competitive total is still eminently possible, if Ross Taylor has his way.
Taylor was unbeaten on 86 when rain ended play in the final session with the visitors at 203-5, anchoring the innings after his teammates couldn't build on solid starts.
The first came from the opening pairing of Jeet Raval and Tom Latham, who added 64 in 26 patient overs to set an excellent platform in the opening innings of New Zealand's World Test Championship campaign.
They looked to have seen off any imminent dangers after skipper Kane Williamson claimed what profiled as a vital toss victory. Teams batting first have won 17 of the last 19 tests in Sri Lanka, with no side having successfully chased more than 100 when batting last.
So, with Raval and Latham going along steadily, everything was going to plan, until Dananjaya struck. The 25-year-old turned the ball both ways with a canny mixture of deliveries, and completely changed the complexion of the innings after being introduced into the attack in the eighth over – a sign of how important spin will be during this test.
Both sides opted to select three spinners, with New Zealand plumping for Mitchell Santner, Will Somerville and Ajaz Patel, to go alongside two seamers in Tim Southee and Trent Boult as Colin de Grandhomme, Neil Wagner and Todd Astle were left out.
New Zealand's spin trio will do well to follow Dananjaya's lead. First, he drew Latham to hang his bat needlessly outside his off-stump, feathering an edge and departing for 30, and, in what will always be a surprise to witness, Williamson couldn't steady the ship; the skipper tossed overboard after just three deliveries.
Attempting to turn a Dananjaya delivery legside, Williamson was caught in two minds, eventually deciding to play off the back foot. However, the ball stuck and spun, and the deceptive bounce left Williamson popping up a catch to gleeful opposing captain Dimuth Karunaratne at short mid-wicket.
Dananjaya's pre-lunch tear wasn't done either, with Raval fooled by a googly, mustering an unconvincing prod, which was taken low at slip, and reducing the Black Caps to 71-3 at the break.
It left a recovery effort for Taylor and Henry Nicholls, and they did a stellar job, counter-attacking after the interval. Taylor's footwork and aggression spread the field, aiding Nicholls, who swept well early on. Taylor had his customary runout scare – a good throw would have had him well short on 37 – but went on to reach 50 for the 49th time in tests.
Nicholls fell eight runs short of his own half-century, trapped lbw missing a sweep immediately after the pair reached a century stand. He wasted a review, on Taylor's recommendation, something BJ Watling wasn't tempted to do when he was also dismissed lbw by Dananjaya, just 12 balls later.
Taylor remained though, easily accumulating off wayward spinner Lasith Embuldeniya, with Santner also unbeaten on eight when rain fell eight overs into the final session. With a reasonably long tail in tow, the Black Caps' lower order will need to support Taylor in his quest of building a competitive total, but – most crucially - also find a way to negate the dangerous Dananjaya.