The fire, which started last Thursday, destroyed an essential oil distillation facility, Mazeikiu nafta reported.
The company said the refinery is currently operating at minimum capacity, refining 15,000 tons of crude a day, compared with an average of 27,400. It said the slowdown could continue for the next six or seven months.
The company's 2006 net profit is expected to fall by 30.5 million euros as a result, its press service said.
Mazeikiu naftà comprises the eponymous oil refinery, with an annual capacity of 12 million metric tons, an oil terminal at the port of Butinge, with an annual capacity of 8 million tons, and an oil pipeline.
In May, Russia's LUKoil [RTS: LKOH] sold its stake in Mazeikiu naftà (53.7%) to the Polish PKN Orlen concern for $1.49 billion.