The recreational boats Karaka and Michelle were rafted up together and both sunk at their mooring at Beach Harbour in Breaksea Sound, prompting Environment Southland to activate its oil spill response team.
The Karaka is an 80-foot former oyster boat and the Michelle is understood to be a former fishing boat.
Several years ago the Karaka sank at her mooring in Deep Cove and was successfully salvaged.
A small amount of diesel which escaped from the vessels is understood to be dispersing naturally in strong winds and choppy seas, Regional On-Scene Commander Dallas Bradley said.
There is understood to be very little diesel aboard either boat, but the owner has agreed to give priority to preventing any further fuel escaping.
The owner had arranged for divers and salvage company representatives to fly in to the site tomorrow.
Mr Bradley said no-one has been aboard for 4-5 weeks and there are no details about what caused the boats to sink.
He had been in touch with the Department of Conservation and established that there are no significant pockets of wildlife to cause concern in the immediate vicinity.