Former oyster boat Karaka and former fishing boat Michelle were rafted up together in Beach Harbour, when they sank at their mooring.
It is believed the boats filled with rainwater. Salvaging them will cost each boat owner an estimated $300,000 to $400,000.
An Environment Southland spokeswoman said no-one was aboard the boats at the time or had been on board for over a month.
Regional on-scene commander Dallas Bradley said a small amount of diesel from the vessels had dispersed in strong winds and choppy seas, but he understood there was "very little" diesel, about 100 litres, aboard either boat.
The owner of Karaka, Craig Harpur from Te Anau, has arranged for divers and salvage company representatives to fly in to the site today to ensure no more fuel escapes.
Mr Harpur suspects the boats fell victim to heavy rainfall on Thursday night.
"It's a real possibility they filled with water and one took the other down with it." Mr Harpur is one of Fiordland's salvage masters and will have to attend to his own boat, starting this morning.
Several years ago Karaka sank at its mooring in Deep Cove and was successfully salvaged.
