The Tamil Nadu government invoked POTA against him after his alleged statement in support of the LTTE at a meeting at Thirumangalam near Madurai on June 29.
Amidst very tight security arrangements, a special police party led by Madurai Rural Superintendent of Police Ayushmani Tiwari executed the non-bailable arrest warrant against the Sivakasi MP, soon after he came out of Chennai airport.
After his arrest, Vaiko was taken in a police van to Thirumangalam near Madurai, about 350 km from Chennai, for production before a judicial magistrate for remand.
Cases had been registered against Vaiko and eight others under POTA, Unlawful Activities Act and IPC.
Vaiko had come to Mumbai from Chicago early on Thursday.