Talley's says the cost of repairs to the Amaltal Columbia will be expensive.
The vessel, which had been fishing off the coast of Canterbury, caught fire at 5.20am on Wednesday about 70km north-east of Lyttelton Heads and had to be abandoned at sea.
The Amaltal Columbia was towed into Port Lyttelton just after midnight with a fire still burning in its factory deck. It was put out after about three hours.
Talley's said on Thursday there is extensive damage to the factory deck of the Amaltal Columbia, but the fish catch was not damaged.
Nelson division chief executive Tony Hazlett said the fire started in the fish meal bagging room and was contained within one deck.
Mr Hazlett said the vessel will be used for fishing again, but the cost of fixing it is unknown.
He hopes the Amaltal Columbia will be operational again in about four months.
Mr Hazlett also said the fish is most likely been unaffected and will be unloaded at Lyttelton.
Most of the crew have been flown home already and all will be redeployed throughout the company's fleet.
Trawler accusation rejected by Sanford
Sanford is rejecting any suggestion it failed to help when another company's trawler issued a mayday call after it caught fire and had to be abandoned.
Radio New Zealand earlier reported that a Korean flagged fishing boat, the Pacinui, which was chartered by Sanford, was in the area at the time the Talley's vessel, the Amaltal Columbia, caught fire.
The Pacinui was claimed to have headed away from the scene, in contravention of maritime law.
Sanford said that is not correct.
Managing director Eric Barratt said another Sanford vessel, the San Discovery, was closer to the drama and went to help instead.
It went to the Amaltal Columbia, picked up some people, took them to Lyttelton and then returned to the vessel and took it in tow.
The Pacanui went on to Timaru.
The Amaltal Columbia was towed into Lyttelton by the San Discovery shortly after midnight and the fire is now out.
A mayday call was broadcast at 5.40am on Wednesday after Talley's flagship caught fire at sea, about 70km north-east of Lyttelton Heads.
The crew were safely brought into Port Lyttelton later in the day.
Investigators will inspect the trawler on Thursday and interview the crew and company officials to find out why it caught fire.
The inquiry is expected to take a year to complete.