RETIREMENT funds for staff at Goldman Sachs and the Commonwealth Bank have topped an official list of the nation's best-performing super funds, as non-profit and in-house corporate funds maintain their track record of higher returns.

In contrast, funds offered by banks and wealth managers to the general public have underperformed over the past decade, according to a snapshot of the $1.4 trillion sector.

The fund for Goldman employees enjoyed average returns of 9 per cent a year since 2004, more than any other large fund over the past nine years, the financial regulator said on Wednesday.

The second-best performer was the CBA's staff fund, which returned 7.8 per cent a year. In third place was the fund for Worsley Alumina workers, with annual returns of 7.5 per cent.

The rankings were published by the Australian Prudential Regulation Authority, which also said super funds had posted average returns of just 0.5 per cent in the year to June 2012, as weak markets hit balances.

In the decade to June, super funds returned an average of 4.4 per cent a year. But there has been a significant gap between different types of funds.

Public sector funds have been the best performers, returning 5.5 per cent, while union-linked industry funds returned 5.1 per cent and in-house corporate funds 4.8 per cent.

Higher-cost retail funds - including those offered by the big banks and AMP - have underperformed with 10-year returns of 3.4 per cent.

The chief executive of the Australian Institute of Superannuation Trustees, Fiona Reynolds, said the gap between the retail funds and non-profits was ''nothing to be sneezed at''.

''Over a 30 to 40-year working life of superannuation contributions, an outperformance of 1 or 2 per cent every year can make a very big difference to an individual's retirement outcome,'' said Ms Reynolds, who represents the not-for-profit sector.

APRA's snapshot of the 200 biggest funds found the best-performing retail fund over nine years was the Tidswell Master Superannuation Plan, in fourth place with annual returns of 7.1 per cent. Perpetual's WealthFocus Superannuation Fund was the only other retail fund in the top 50 funds over nine years.

Unisuper was the top-performing industry fund, in equal fourth place, while the Australia Post Superannuation Scheme was the best-performing public fund.

Despite posting weaker returns over nine years, retail funds have fared much better over the past five years, occupying the two top spots on the ladder.

Challenger's Retirement Fund was the top performer over five years, returning 4.7 per cent a year, followed by Newcastle's Permanent Superannuation Plan.

In the competitive market to manage the public's retirement savings, APRA's ranking tables are not without their critics.

The investment research manager at consultancy Chant West, Mano Mohankumar, said they did not take into account the individual products offered by each fund, which often had different goals.

''It's not comparing like with like, and no one actually invests in the whole of fund,'' he said.

Since June last year, super funds have enjoyed a sharp market rally, with analysts estimating the typical fund delivered double-digit returns over the 2012 calendar year, helped by a market surge in the December quarter.