A section of the protestors also set the Sri Lankan national flag on fire, besides burning the portraits of Rajapaksa on Parliament Street here.
Addressing his supporters, Vaiko, whose MDMK is part of the NDA, said the presence of Rajapaksa would "pollute the sanctity" of Modi's swearing-in ceremony.
He also alleged that the Lankan President had committed genocide against the Tamils in the island nation.
He also appealed to the NDA not to follow the path of the UPA Government on the Sri Lankan issue.
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"I hope Narendra Modiji and his Government will understand the pain in our minds and the crime committed by the Sri Lankan Government with the help of the UPA Government," he said.
However, Vaiko clarified that he was not against the NDA Government and greeted Modi, who is set to sworn in as Prime Minister today.
Vaiko, along with his supporters, was later taken into custody for defying prohibitory orders.
The MDMK chief had earlier written a letter to Modi expressing his sadness over the invitation being extended to Rajapaksa for the event.
Recalling that no Sri Lankan Head of State was invited when A B Vajpayee was sworn in as Prime Minister, Vaiko had pointed out that even Manmohan Singh had not invited the Sri Lankan President for his swearing in ceremony.
The Sri Lankan President arrived this morning for the ceremony.