Dr Walker said the trial was a huge coup for the Lakes District Health Board area, which had higher smoking rates for Maori than the national average.
She said the study focused on Maori because their rate of smoking was so high, and they potentially had the most to gain from getting help to quit.
The study has just received $1.6 million funding from the Health Research Council - one of the largest grants. At the moment cytisine is only used in two countries in Eastern Europe where the natural substance is derived from plants.
"We want to find out if the proportion of people who successfully stop smoking after taking cytisine is similar to those taking varenicline. If cytisine is effective, has an acceptable safety profile, and is cost-effective, it has substantial potential for use as an alternative treatment to help people quit smoking."
Dr Walker said the Lakes area was chosen because of the high rates of smoking and because of the involvement of study team member Dr Barry Smith, who is based at Lakes District Health Board.
She said the recruitment process was likely to start in November. The recruitment phase would take about 18 months and participants would be followed for six to 12 months, with results available in about three years.
Health board communications officer Sue Wilkie said getting funding for the trial was both "important and exciting" as "the health of Maori is a key focus of the Lakes District Health Board and its iwi governance authorities". Health board Pou Herenga Maori Health Eru George said the initiative had a great potential for improving Maori health in the Lakes region and elsewhere.