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The Performance of Manufacturing Index (PMI) scored the sector at 56.3 points for last month, up from 37.9 in August.
A PMI reading above 50 indicates that manufacturing is generally expanding; below 50, it is declining.
The index found production levels were above 60; new orders, employment levels and stocks and finished products were above 50.
Deliveries of raw materials were less than 50.
There were 54% positive comments for the month.
"There was mixed feedback, which included both positive and negative reactions in construction, wood and paper product manufacturing along with machinery and equipment manufacturers," Otago Southland Employers’ Association chief executive Virginia Nicholls said.
"Some food manufacturers experienced less sales due to the regional Alert Level 3 in Auckland."
Food/dairy exports were steady and there were concerns about increased airfreight costs.
Aluminum boat manufacturing was steady.
The long-term uncertainty around Covid-19 has raised concerns, Mrs Nicholls said.
"There are concerns with filling some skilled and unskilled roles. A safe, open border is crucial to NZ’s export success," she said.
"A pipeline of skilled and qualified workers is critical to New Zealand’s Covid-19 recovery, but we are struggling to get them into the country."
She said there were major concerns as the start of the horticultural season approached with a distinct lack of seasonal workers.
"Despite some good campaigns to get New Zealanders to cover the RSE workers, many believe it will be difficult to replace these experienced workers from the Pacific with short-term workers."
Businesses were increasingly frustrated with delays at an overwhelmed Immigration New Zealand, which have worsened since Covid-19.