The demonstrators, among them Parti Socialist Malaysia activists, had walked into the Customs headquarters in Kelana Jaya at 11am demanding answers to 106 questions relating to the GST.
They wanted to speak to and hand over a memorandum to the Customs director-general on the tax regime.
Police, along with the FRU, later barricaded the office complex and barred anyone from entering with a group of protesters still inside.
At least 80 people were later taken away in a police truck at the end of the protest.
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