His individual at-risk pay fell from $124,705 to $119,170. But it was the pay linked to the fund's returns that took the biggest hit.
A bonus based on the fund's excess return on a four-year moving average was just $57,209 compared to the prior year's $78,917.
A "value add" bonus also based on a four-year moving average was $39,993, down from $153,220.
Whineray also received $68,087 in contributions towards his KiwiSaver scheme and $5593 in benefits from having life, income protection, trauma and health insurance paid for.
The Super fund had a return of just 1.73 per cent during the year to June 30 after it was hit by the market downturn caused by Covid-19.
Over the past 10 years it has averaged 12.6 per cent per annum in returns.
Chairwoman Catherine Savage said in her annual report statement that between January and mid-March the fund's value dropped significantly in line with global equity markets but it had recovered since then, rising $1.7b in the financial year.
But she said despite the volatility in markets the crisis did not present a major risk to the fund.
"As investors, we are advantaged by our endowments; we have a long-term investment horizon with no substantial withdrawals until well into the 2050s.
"Our investment strategy and portfolio choices are designed with this in mind and the fund is well placed to weather and even benefit from the volatility we are experiencing now."
Savage said while markets had recovered quickly in recent months, both the local and global economy may continue to be "severely challenged by the current crisis and will take many years to recover to pre-crisis levels".
"Companies' business models will need to change and many will not survive in their current form."
Chair to depart
Savage said this would be her last annual report as she would be stepping down from the board in March 2021 after more than 10 years.
"Over this time the Guardians has come a long way, and it has been pleasing to see its investment frameworks, governance and internal capability developed to best-practice
standard and to be recognised as such.
"I have valued the experience, the people I have served and worked with, and the opportunity to lead an organisation committed to furthering the financial wellbeing of future generations of New Zealanders."