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Clicks says protest action is currently happening at 37 stores across Kwa-Zulu Natal, Gauteng, Western Cape and also in the Eastern Cape.
Seven stores were damaged including Saveways in Witbank, Cycad in Polokwane and Algoa FM News has learnt that Clicks in Komani was also damaged.
The company says it has taken full responsibility and apologised unreservedly for the advertisement published on its website and has taken immediate action to address all concerns.
Stores in different centres in the Eastern Cape have been closed in the wake of the call by Economic Freedom Fighters leader, Julius Malema.
His call on members to, as he put it, "Attack", came in response to a racist advertisement on the store's website for a hair product by the company TRESemme'.
Clicks and TRESemme' have since issued apologies for the ad, with CEO, Vikesh Ramsunder, saying he was deeply disappointed that this was allowed to happen on their website.
The South African Police Service says members of the Public Order Policing Unit are also monitoring the situation.
Clicks meanwhile say it will be taking all the necessary precautionary steps to ensure the safety and well-being of its customers and employees.