The 12,400-ton factory ship Chernomorskaya Slava was anchored outside Lerwick harbour with a fire raging among 100 tons of cardboard boxes used for packing fish.
A spokesman for Highland and Islands fire brigade said: 'We are beginning to realise that this is going to be a long, protracted incident.'
Fire crews from Aberdeen and Orkney were being flown by helicopter to Shetland to relieve fire fighters who had been working since Thursday night.
Two fire-fighting tugs were standing by the ship spraying the hull to keep it cool. More than 100 factory workers were evacuated, leaving the ship's crew of around 50 on board.
The spokesman said: 'Our tactics are to batten down the hatches and flood the hold with high expansion foam. Every so often we open the hatch to find out the state of the fire.' No one has been injured.
Lerwick lifeboat was continuing to ferry equipment to and from the shore, while Shetland coastguard's rescue helicopter was on standby at Sumburgh airport.
There was no indication as to how the fire may have started.
It broke out on Thursday on the ship as she lay at anchor one mile north of the island of Bressay, within sight of Lerwick harbour.
The ship had been in the area for the past three weeks during the herring season and had been taking on fish from local boats for processing.Reuse content