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The problems included some households still not having received their three plastic bins more than two weeks after the new system began on July 1, and a rat problem in Queenstown's materials recovery facility.
Property and infrastructure general manager Peter Hansby said the facility had ''needed a lot of attention since being transferred back from the previous operator''.
The new operator is Waste Management, and Mr Hansby said repairs to the facility had been necessary, and there had been rats.
''Due to unseasonably warm weather, rats have also added to the challenges at the materials recovery facility site.
''Although rodents aren't an unusual visitor around rubbish and recycling, the increased volume is a health and safety hazard and [the council] has had to fumigate the facility.
''We and the previous operator, Smart Environmental, were aware of the rat problem ...
it's added to further delays in getting the facility up and running for Waste Management.''
As well, a ''handful'' of households had not yet received their bins.
''With a massive task to undertake, changeable weather conditions and some glitches in data around newer homes, it's disappointing but perhaps understandable why not everyone got their bins for July 1,'' Mr Hansby said.
''The project team are working to complete their deliveries as soon as possible.''