New Zealand still have plenty of work to do despite taking a 55-run lead into the second innings of the second Test against Pakistan on a rain-affected day in Hamilton, says Tim Southee.

Southee led the Black Caps bowling attack well on Sunday as he claimed his first five-wicket haul at his home ground to help dismiss the tourists for 216, Babar Azam the only thorn in their side with an unbeaten 90.

His 6-80 ensures the hosts have a healthy first-innings lead heading into day four, although their progress has been hampered by the weather on the North Island.

Despite their advantage Southee knows there is still a lot of work for the Kiwis to do if they are to complete a 2-0 series win, with the conditions likely to help the Pakistan seamers.

"In no way do we think the job's done, or anywhere near done," he told a media conference.

"Taking a 50-odd run lead into the second innings after losing the toss on that wicket, I think we're pretty happy with how the situation sits at the moment.

"We know that they've got some quality bowlers in their line-up, and with a wicket that's still offering a little bit with the new ball, we know that we're going to have to come out and bat well if we want to get into a decent position in this game going forward."

Southee admitted he was out of sorts early on as Sarfraz Ahmed in particular dished out some punishment, but he used his knowledge of the Seddon Park wicket to come back and take his tally for the series to 11 wickets.

"I play a lot here, and it's always nice because it's one of the few grounds in the world where the wind actually assists a right-arm outswing bowler," Southee added.

"Personally I was a little bit off in that first spell, the rest of the guys bowled pretty well throughout that first innings. There were five overs in the start of the day where we missed a little bit. 

"They [Pakistan] had a positive mindset and put the bad balls away. The nature of Sarfraz is that he's an aggressive player. If you do miss, he's going to look to put it away. We did that a few too many times."