"We didn't predict the extent of the impact the vaccination schedule would have on these groups," Dr Petousis-Harris said.
"The greatest improvements were seen amongst children from groups that carry the greatest burden. This is a very positive result."
Maori and Pacific people have rates of the disease three and four times higher than the general population.
After the vaccine's introduction, researchers found ethnic disparities in hospital admission rates were reduced, with invasive pneumococcal disease down by 70 per cent among Maori children.
Pneumococcal disease causes serious and potentially deadly illnesses, including pneumonia, meningitis and blood infection.
Invasive pneumococcal disease occurs when bacteria pass into blood, inflame the membranes around the brain, or infect other sites such as joints.
The vaccine covers most strains of the disease that cause serious illness in young children.
Since 2008, hospital admissions of children under 6 for invasive pneumococcal disease have halved, while cases in children under 2 have dropped by 81 per cent, the studies found.
Disease strains targeted by the vaccine have been almost eliminated - there has been just one case in 2013.
Notified cases of invasive pneumococcal disease fell from 697 cases in 2009 to 479 cases in 2013.
Under the New Zealand childhood immunisation schedule, children are given four doses of the vaccine at six weeks, three months, five months, and 15 months.