Over the year to March 2021, gross domestic product fell by 2.3 per cent, also reflecting the impact of Covid-19 restrictions.
Just two industries recorded increases in emissions over the year.
Electricity, gas, water, and waste services increased 13 per cent and services excluding transport, postal, and warehousing increased 0.3 per cent.
"Electricity, gas, water, and waste services emissions were up due to the greater reliance on fossil fuel use for electricity generation over the year, as New Zealand experienced dry conditions in hydro-generation areas," Oakley said in a statement.
The June 2020 quarter saw the largest decrease in emissions, down 7.6 per cent due to a combination of lockdown and border restrictions.
The largest contributors to this drop were transport, postal, and warehousing and households.
Emissions rebounded by 8 per cent in the September 2020 quarter as restrictions were lifted.
In the March 2021 quarter, emissions rose 1.1 per cent as economic activity recovered after the fall in activity and emissions in the December 2020 quarter.
New Zealand went into a level 4 nationwide lockdown on March 25, 2020.
The alert level was lowered to level 3 in April, and to level 2 in May.
The country moved to level 1 on June 8, removing all remaining restrictions except border controls.
It is the third time Stats NZ has produced quarterly experimental estimates of New Zealand's gross emissions on a United Nations System of Environmental Economic Accounting (SEEA) basis.
The statistical framework has been endorsed by the United Nations, OECD, and IMF, and it is used by over 70 National Statistics Offices for a range of accounts, Stats NZ said.