The company's processing fee revenue was also hurt by a kiwi dollar that averaged 82 US cents in the first half, up from 80 cents a year earlier.
While the company's margins continued to improve in July, the recovery isn't expected to be sustained, Jackson said.
"There is still an excess of capacity in global refining and this will drive further margin volatility while the relative strength of the New Zealand dollar continues to pressure our earnings," he said.
The shares last traded at $2.25 on the NZX, valuing the company at $630 million, and have declined 11 per cent this year.
His comments were echoed by chief executive Sjoerd Post, who described refining in the Asia Pacific region as "ultra-competitive, with new capacity coming on stream and more to come."
NZ Refining can influence its customer choices by "continuing to produce high quality 'on spec' products", a focus on reliability and "being more competitive on price," Post said.
NZ Refining will pay a first-half dividend of 2 cents a share, unchanged from a year earlier.