"During shutdown flaring is a crucial safety precaution that involves the releasing of pressure and safe venting of hydrocarbon gases," he said.
"Such an unplanned and high visible event is the last thing we want for the safe and reliable running of the refinery."
The fault was expected to cost Refining NZ up to $8 millon in lost revenue. A fix on the hydrocracker had been carried out on March 19, though it was still running at a reduced rate, with a full fix expected to coincide with a routine maintenance shut down from April 1.
Mr McNeill said the flaring was in line with the company's emission consents, but that Refining NZ worked to minimise any negative effects on the local community and environment.
"While flaring is nowadays a relatively rare occurrence, it is nevertheless a process we use to safely shut or start our operations ... The limited smoke that sometimes accompanies flaring is comparable with what ships on the harbour emit."
Northland Regional Council's regulatory services manager Colin Dall said there were clauses in Refining NZ's consent that allowed for emergency flaring. Yesterday he could not confirm whether the most recent incident was in line with the consent, as the staff member in charge of air quality was away.
Whangarei district Bream Bay Ward councillor Shelley Deeming said she supported the refinery.
"They've got consents to handle any mishap. Yes, it's unfortunate but in the end we really need the economic development [the Refinery] brings," she said.
Cr Deeming said the flaring did not appear to have caused much alarm among her other constituents.
Whangarei Heads resident Harvey Gadd photographed some of the flaring from his Reotahi home, but said it did not bother him because wind direction meant his area was largely unaffected.
"Personally, I'm not concerned about it, it's obviously necessary. But I can see why some people might have complained."