Shanks (26) was edged out by Olympic silver medallist Wendy Houvenaghel, of Great Britain, in the final of the women's 3000m individual pursuit, reversing their close result from the world championships in Poland earlier this year.
The Great Britain rider edged out Shanks in the closing lap to win by 0.38sec in 3min 33.771.
Shanks said it was a close race, with the lead alternating throughout the race.
"It was a pretty good race for the crowd to watch and I think it was only on the last lap that she managed to get in front," Shanks said.
"But considering it is early season and I'm looking at the big picture, with the world championships in March and then the Commonwealth Games in October, I can't be too unhappy with what happened."
She said the time reflected the cold conditions inside the air-conditioned velodrome.
Her time was expected after times recorded in training, and the positive was her performance was way ahead of where she was at the same time last year.
Shanks contests the team pursuit tonight before competing in the team race at the Lake Taupo Challenge, a 160km race around Lake Taupo, next Saturday.
She will then return to training, but shortly afterward a meeting in Europe may decide if she can chase Olympic gold in the individual pursuit in 2012.
Cycling's governing body, UCI, will deliver proposals to the International Olympic Committee next month for a track race programme at the 2012 London Olympics which offers equal gold medal opportunities for men and women.
The governing body will risk upsetting riders and national teams by cutting traditional races to create the balanced schedule, with the possibility of the individual pursuit and the points races being axed.
Shanks admitted the move to axe the pursuit was out of her control and there was not much she could do about it.
"I talked to Wendy [Houvenaghel] about it and she would be as gutted as me if they did get rid of it . . . the individual pursuit is a blue riband event, so it is hard to fathom why they are trying to get rid of it.
"There are things like the numbers of athletes at the Olympics and there's always politics around these sort of things.
"Hopefully, if they still have a team pursuit then they can have an individual pursuit alongside it."
A proposal will be put to the IOC's executive board on December 9-10 in Lausanne, Switzerland.
Fielding cyclist Jesse Sergent (21) went one better than Shanks on Thursday night, winning the men's 4000m individual pursuit with a time of 4:23.192, finishing more than a second ahead of Australian Rohan Dennis.
