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It said in a statement the de-registered union was the South African Clothing and Textile Workers Union, which also used the acronym Sactwu.
"Regrettably this confusion has caused some serious confusion among employers and workers in the clothing and textile industries," the union said.
"This debacle needs to be clarified urgently as it could have serious implications and cause severe negative consequences for industrial relations."
On Tuesday, Labour Minister Membathisi Mdladlana announced his department had de-register more than 150 unions and employers' organisations that were either bogus or had failed to adhere to labour law requirements.
Sactwu said Mdladlana had explained the two unions were not the same.
"I must also point out that the cancellation of registration of the South African Clothing and Textile Workers Union with the registration number LR 2/6/2/436 should not be confused with the Sactwu that remains a registered union," Mdladlana said.
"Although the two unions have the same name, the former was registered in terms of the legislation of the former self-governing area of KwaZulu-Natal."
