Trans Pacific Industries won the tender to service the collection of about 135,000 bins from Pt Chevalier, Avondale and Blockhouse Bay in the west though to Tamaki Estuary, Glendowie and Otahuhu in the east.
The company started the new contract, which also included the collection of street litter bins, on July 1.
"It was anticipated that the contractor's newness to the collection routes and timings would require time to get up to speed," said Auckland Council waste operations manager Warwicke Jaine.
Mr Jaine said the electronic system to provide drivers with their routes had also been incorrectly programmed. He said the software issue had been rectified and extra trucks were added throughout the week solely to collect missed service collections.
"We are confident the contractor is properly resourced for the service levels required, and driver familiarity will continue to improve week to week."