The men were apparently swept off the rocks near Slope Point Rd and have been missing since 4pm yesterday.
A police spokeswoman said this morning a witness had seen the pair n the water.
"He did not see them actually get washed off the rocks, but they had been there prior."
About 4pm today, police said team members in the IRBs had completed a shoreline search.
A helicopter was continuing to search the area, while the LandSAR team would continue on foot until low light. Police would continue to monitor sea and wind conditions.
The spokeswoman said police have been in contact with the families of the missing men.
"We're not in a position to name the fishermen yet, but we know who they are and were able to speak to family members yesterday."
Slope Point is the southernmost point of the South Island, and is notorious for its rugged coastline and rough seas. It lies just south of Waikawa and Haldane, near the southwestern edge of the Catlins, and is 71km east of Invercargill.
Rescue helicopters from Queenstown and Dunedin were involved in the search, as well as swimmers, several boats and three Land Search and Rescue teams.
Bad weather and poor visibility forced police to scale back the search last night.
This morning, about 11 rescuers in high visibility vests were seen by the an Otago Daily Times reporter walking along the coast. Two IRBs could be seen offshore conducting a search. Much of the area where the search was being carried out was only accessible to 4x4 vehicles.
A police spokesman said earlier that a large search and rescue crew had been deployed about 6.20pm yesterday, including two rescue helicopters from Queenstown and Dunedin, rescue swimmers, the Bluff Coastguard, a Bluff Harbour pilot vessel and Catlins water rescue teams, along with three Southern region LandSAR groups.
The helicopters had to be stood down earlier in the evening, but land and water-based search crews continued "in a limited capacity" until about 10pm.
The search was hampered by heavy rain and 2m swells in the area yesterday.
- By staff reporters; additional reporting by RNZ
