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The company's refinery at Marsden Point processed 22.56million barrels of oil in the second half of last year, 4% more than a year earlier and an all-time record for the period.
That left total throughput for the year at 40.44million barrels, 3% less than the year before. Volumes in May and June were roughly halved during the site's biggest shutdown in 15 years.
The firm's shares were recently unchanged at $2.39. They have fallen about 9% in the past year.
The plant at Marsden Point is the country's only oil refinery and produces about 70% of the petrol, diesel and jet fuel used in New Zealand. Forty-three percent of the plant is owned by Z Energy, BP and Mobil, and it charges those customers processing fees based on refining margins in Singapore.
Those fees fell to $258.7million for 2018, $70million less than the year before, reflecting lower regional margins for most of the year and the loss of production from the longer-than-expected shutdown.
Average margins fell to $US6.31 ($NZ9.34) a barrel from $US8.02 the year before, when the company reported a full-year profit of $78.5million.
That was on $411.7million of operating revenue, including almost $82million from the plant's distribution activities, natural gas recovery and leases.
In August the company reported a $2.8million first-half loss and said the shutdown would reduce full-year profit by about $43.2million.
The firm, which trades as Refining NZ, has a raft of upgrade projects under way since completing the installation of the $365million continuous catalytic regeneration unit in late 2015.
It continues to invest to ensure it remains competitive against larger, more modern refineries its customers can also buy product from.
With no major shutdowns planned in 2019, the company has previously signaled it could process a record 44million barrels this year.
The record was 42.67million barrels in 2016