The violent protests in Hout Bay on Sunday may have been sparked by a misunderstanding regarding an anti-poaching operation, the Department of Agriculture, Forestry and Fisheries (DAFF) said.
"None of the DAFF officials assisted, but they were on standby. The special task force arrested two suspects at sea and one suspected poacher jumped overboard and is still missing," DAFF spokesperson Khaye Nkwanyana said.
A fishing boat with crayfish and fishing nets were seized during the operation.
"The suspected poachers presumed that one of our officials Bernie Smal had been instrumental in the operation. Today, a huge crowd stormed Hout Bay harbour and burnt two of our offices and another group went to our official's house and set it alight."
Nkwanyana added that police have taken Smal and his family to a place of safety.
"The police will continue to maintain public order in the area and we have organised private security to guard Mr Smal's residence and our property in the harbour," he said.
GroundUp identified the missing man as 25-year-old Deurick van Blerk who had been catching crayfish illegally with three other men when they were intercepted by a DAFF patrol vessel.
Police spokesperson Lieutenant Andre Traut said that a missing person docket was opened by Van Blerk's family when he failed to return home on Saturday.
Three suspects were arrested for public violence and provincial detectives are probing a case of public violence after the buildings were set alight, he added.
A source in Hangberg, who asked to remain anonymous, told News24 that protestors had disrupted the Hout Bay market earlier in the day. The market had to be shut down and shoppers were evacuated from the premises.
The crowd dispersed at 15:00 and returned to Hangberg where they continued to fire flares.