Throughout the rest of New Zealand, 77 per cent of rent was paid by its due date, compared to the monthly average of 83 per cent.
Re-Leased chief executive Tom Wallace said landlords had been understanding and providing rent holidays, but smaller landlords may be feeling the pressure.
"In many cases a landlord might be a couple who operated that business, they may have operated that store and it may have been their life's work for 20-30 years and they maintained the property and leased it out.
"Those are the sorts of people that can really struggle and it can really impact them because they rely on that income to live."
Wallace said the retail sector was struggling the most.
In Auckland, just 54 per cent of commercial rent was collected by its September due date, compared to 77 per cent pre-lockdown.
Outside Auckland, they were 75 per cent and 86 per cent respectively.
"The 2021 lockdown has clearly impacted tenants' ability to access their premises, in particular those in the retail sector, which has a knock-on effect for landlords in longer collection times and larger amounts of rent written off for consecutive months," Wallace said.