Waste Management said the incident would not affect its service to customers, as another truck from Christchurch would arrive in the city this morning.
Firefighters were called to the rubbish blaze in the rear of the truck in Graham St, about 10am yesterday.
Station officer Simon Smith said the truck's driver noticed smoke coming from the vehicle while on his rounds.
''He tried to extinguish it with an extinguisher but it was a bit much, so he called us,'' Mr Smith said.
The firefighters, from Dunedin Central station, cut holes in the truck to enable water to get in.
The truck was towed to Waste Management's Wickliffe St site, where a crane was used to open the vehicle so firefighters could douse the smouldering rubbish.
It was unclear exactly what caused the blaze as ''there's three and a-half tonnes of rubbish in there'', Mr Smith said.
The truck received ''quite substantial damage'' as a result of the fire.
Waste Management national customer manager Marsha Cadman said the company would have a better indication of what caused the fire once its contents had been inspected by the Fire Service.
The truck's driver suffered no injuries or smoke inhalation as a result of the blaze, but it was a reminder for people to be cautious about what they disposed of in the rubbish, she said.
