The number of hours worked rose by 15 million or 0.9 per cent.
"Extended lockdowns in New South Wales, Victoria and the Australian Capital Territory have seen employment and hours worked both drop back below their pre-pandemic levels," Australian Bureau of Statistics head of labour statistics Bjorn Jarvis said.
In September, there were 111,000 fewer employed people and two per cent fewer hours worked than in March 2020.
"The low national unemployment rate continues to reflect reduced participation during the recent lockdowns, rather than strong labour market conditions," Mr Jarvis said.
Earlier, Reserve Bank of Australia deputy governor Guy Debelle said the central bank was not seeing any material changes in wages or inflation that would pave the way for a tightening of monetary policy.
Last week, the Reserve Bank of New Zealand lifted its key interest rate, while the US Federal Reserve is mulling whether to pull back on its stimulus.
"The circumstances here in Australia ... both wages and inflation, are quite different from those we are seeing in other countries," Dr Debelle told an online conference on Thursday.
Australia went into the pandemic with persistently low wage outcomes - much lower than what was being seen in comparable countries.
"COVID hasn't changed that picture. The story on the wage front hasn't really changed in any material way," he told the CFA Australia Investment Conference.
"Yes, there are a few pockets of heightened wage pressures, but it's not widespread."
Similarly, on inflation, he said Australia is not quite experiencing some of the energy issues that have been seen elsewhere in the world, although that is flowing through to the oil price.
And there had not yet been much impact from supply chain disruptions feeding into prices.
The RBA has persistently said it will not lift the cash rate until inflation is sustainably within the two to three per cent inflation target.
It would need to see wages growth of three per cent, compared with 1.7 per cent currently.
It does not expect these conditions to be met before 2024.