Smith, 22, had been in rehabilitation since last month's NAB Challenge match against Fremantle and on Wednesday left the track after some running exercises.
Assistant coach Darren Crocker said Smith's latest complaint was nothing serious but confirmed that he would miss the first two rounds of the season.
"He was probably never in consideration for a round-one berth," Crocker said from North's season launch at Eureka Tower.
"He had a slight hiccup obviously in the Fremantle game.
"If that hadn't have occurred and we had have been able to get games into him again against Port Adelaide and Essendon, he would have been in calculations for round one.
"He's probably two weeks behind where we would have liked him to be. So we're talking hopefully round three or round four."
Crocker said Smith's hamstring wasn't torn and that he had an edema – a build-up of fluid in the area which can be caused by inflammation.
"He'd be the first to admit that he's probably very conscious of his body and where it's at," Crocker said. "The twinges and twists that he takes throughout his rehab and throughout his training, perhaps there are times where it sends out a little bit of a scare but there's nothing major to it.
"That's where we need to make sure he trains with intensity so he gets through that period of time and gets his body nice and conditioned."
A hamstring injury limited Smith to just two games last year after he overcame recurring ankle woes. He has played 27 matches since his 2005 debut.
Crocker added that defender Daniel Pratt would not line up in the VFL this weekend and that round-one selection was his focus again.
Pratt, who had major shoulder surgery at the end of last season, was left with rib bruising after a contest with Carlton forward Brendan Fevola in the first week of the NAB Cup.
However, he made a successful return in last Friday's game against the Bombers.
"We talked about him playing in the VFL but felt that we could actually train him up between that game and the first round to get him to a point where he should be able to get through AFL football," Crocker said.
Key forward prospect Robbie Tarrant, onballer Leigh Adams – who missed all of last season with a knee reconstruction – and Irish rookie Conor Meredith will play for Werribee in its practice match against North Ballarat on Saturday.
North's only other injury concern is wingman Matt Riggio, who has battled a stress reaction in his shin for close to a month but should start running again next week.
After seven games in 2008, Riggio was poised to offer more in his fourth year at the club.
"You start to think what was looking like a terrific pre-season is probably starting to go back the other way and he's going to actually have to make up some lost ground," Crocker said.
With the season opener against Melbourne just 10 days away, Crocker said he would be "surprised" if at least one of the club's stand-out draftees, Jack Ziebell and Liam Anthony, wasn't selected.
Dream Team watch – Jesse Smith is rated a $197,000 defender in Toyota AFL Dream Team 2009
Daniel Pratt is rated a $330,100 defender in Toyota AFL Dream Team 2009
