McCullum, troubled with what appeared to be injuries to his left shoulder and right elbow, blasted the only six of his innings over long on off Ishant Sharma to bring up the milestone about 45 minutes before the end of play.
The 32-year-old McCullum was 114 not out at stumps having shared in an unbroken 158-run partnership with wicketkeeper BJ Watling (52) that guided the hosts to 252 for five and stalled India's drive for victory at the Basin Reserve.
"It was hard work out there," McCullum told Radio Sport. "I thought they bowled brilliantly and at five for 90 (odd), things weren't looking so good.
"Thankfully BJ and I put together a partnership which was undefeated at the end of the day."
Corey Anderson was the only wicket to fall during the final two sessions, having joined McCullum at the resumption of play following the lunch break after New Zealand had slumped to 87 for four in the final over of the morning session.
Anderson had tried to work Ravindra Jadeja into the leg-side only to get a leading edge and it ballooned back to the left-arm spinner.
Anderson's dismissal reduced the hosts to 94 for five and in danger of not seeing out a sun-drenched day, before Watling and McCullum dropped anchors and took their side through two sessions to ensure they would be back for a fourth day.
The normally free-flowing McCullum faced 237 balls and had been batting for just under six hours while Watling was even more obdurate with his 52 coming from 208 deliveries. He had been at the crease for more than four hours.
"It's what the team required and as captain that's what you try and achieve," McCullum added. "You're not always going to do it, but you have to try and work your game to the situation.
"I was just pleased to get through to the end of the day with five down. We have got a lot more ground to cover tomorrow."
New Zealand had resumed the day on 24 for one, a deficit of 222 runs, and slumped further into the mire when Zaheer Khan grabbed two early wickets to put India firmly in charge of the match.
The 35-year-old left-armer had the ball move slightly away off the seam to catch the thinnest of outside edges of both Kane Williamson (seven) and Hamish Rutherford (35) to reduce the hosts to 52 for three inside the first hour.
Debutant Tom Latham was then dismissed by Mohammed Shami in the final over before lunch for 29, having avoided the dreaded pair in his first Test when he punched Zaheer through point for two runs.
India must win the match to level the two-Test series after New Zealand won the first game at Eden Park by 40 runs and McCullum said he felt while the visitors were still in the ascendancy the match could still turn the home side's way.
"Being five down was key for us," he said. "If we had been six or seven down I think the Test was over.
"It was a big couple of hours at the end of the day there."
- Sports & Recreation