Tests are being run to determine the level of pollution from the UPL Chemical Plant in Cornubia, Durban.
The agricultural plant was torched on July 12, during a wave of looting and unrest in the area.
Following the burning of the factory, toxic discharge has flown into the Durban North beaches resulting in dead fish.
The eThekwini Municipality has also closed all Durban North beaches as a precaution.
Residents living near Cornubia and Umhlanga have also complained of unbearable toxic smells entering their homes.
In a statement released on Saturday, UPL South Africa said it is unknown at this stage how toxic the pollution is. UPL said there were several fires set off in the area so they are possibly not the only source of the toxic fumes.
"Environmental specialists are taking samples from the Ohlanga river and uMhlanga lagoon to determine if there has been any contamination, and these will be processed as soon as it is possible to transport the samples to laboratories," said the statement.
"It is not known at this stage what proportion of any pollution may be from the warehouse or other sources, but UPL are doing everything they can in the extremely difficult circumstances to protect people and the environment, regardless of the source."
MEC for Economic Development and Environmental Affairs Ravi Pillay, visited the burnt site on Saturday.
SpillTech, an industrial cleaning service, has been deployed to clean up the site.
Pillay said the extent of the damage was over R1 billion.
"They (UPL) are quite emphatic they are not the cause of the smell but of course we are doing tests and analysis and we will get the results next week," he said.
Pillay said he was concerned about the impact on the marine life that has been affected by the toxic discharge.
Pillay added there are signs that water quality is improving in the beaches.
With regards to the unrest, Pillay said he was inspired by the determination of people in the business sector who are starting to rebuild.
"The top two priorities has been opening the N2 and N3 corridors which are now running and the second was the scarcity of fuel supply which is steadily improving," he said.
UPL advised residents living near the Cornubia area to stay inside if they are under a cloud smoke.
Members of the public should contact the eThekwini Disaster Management Team on 031 361 0000 or seek medical attention if they have concerns.