The spokeswoman said it also had a high number of children in its scheme.
"We have a significant number of KiwiSaver customers aged under 18 compared with other new-to-market KiwiSaver providers."
Booster had the second lowest average balance at $12,518 while Westpac Bank's scheme was the third lowest at $13,198.
A Booster spokewoman said it was because it had a high proportion of child members – which has an impact on the average balances and contribution rates.
A spokesman for Westpac also said its low balance was due to a higher proportion of children in its scheme.
"This is because Westpac would have a higher proportion of non-contributing minors than many of the other providers."
The research also showed a big range in the average balances across the country's largest KiwiSaver provider.
ANZ bank, which manages more than $11 billion across its three KiwiSaver schemes, has an average balance of $13,383 in its largest scheme - but an average of $28,921 in its OneAnswer scheme.
ANZ's default scheme has an average balance of $15,644.
Ana-Marie Lockyer, general manager wealth product at ANZ, said the balances in its schemes differed as each scheme had a slightly different membership profile.
"ANZ KiwiSaver has a higher proportion of children and their balances may only include the $1000 kickstart that the government used to pay, and then subsequent investment earnings on top of that."
Lockyer said while its default scheme had a smaller number of children it had a wider distribution of members across the entire working age population.
"A significant proportion of this scheme would have been invested in the default fund, without making an active choice."
People are put in one of nine default funds when they start or switch jobs and are automatically enrolled and do not decide which KiwiSaver fund they want to be in.
Lockyer said as long as the default funds were conservatively invested it was likely those members would have lower returns over the long term and therefore lower balances.
"That is why ANZ investments believes it is so important that KiwiSaver default members review the type of fund they are in to make sure it suits their age and risk profile and recognise that they have been enrolled into a conservative fund temporarily while they consider if it is right for them.
"Over a long period of time this will make a larger difference to retirement savings outcomes."
Lockyer said its OneAnswer scheme was sold via financial advisers and their clients were generally more progressed in their careers with higher earning and savings potential.
"It is also worth noting that many within this scheme would have had conversations with their advisers about the benefits of choosing the most appropriate fund for their age and of maximising their contribution levels."
At the top end Milford Asset Management has less than 20,000 people in its scheme (19,761) but has an average balance of $49,120.
The data was collected by actuaries Melville Jessup Weaver for Workplace Savings - the industry body for workplace superannuation schemes.
The research doesn't include every single scheme but the 20 schemes it covered account for $43.5 billion out of the total $45 billion in KiwiSaver assets as of September 30.
