Tarun Vijay, of the ruling BJP, was speaking to al-Jazeera about recent attacks on African nationals in India.
African envoys have called the incidents racist in nature.
But defending India, Mr Vijay said: "If we were racist, why would we have the south? Why do we live with them? We have black people around us."
The comments triggered an immediate response on Twitter, with many south Indians asking if Mr Vijay was implying that the rest of India "chose" to live with them.
Much of the outrage stems from the fact that there have been historical tensions between northern and southern Indians, based on language, culture and even skin colour.
Mr Vijay quickly tried to carry out some damage control on his Twitter account, saying that he had "framed" the sentence badly and adding that Indians were victims of the "racist British".
What he was trying to say, he said, was that Indians had fought racism and had "people with different colour and culture" but did not have any racism.
However, Mr Vijay's attempts to explain did not seem to convince too many people, who continued to ridicule him.
A spokesman for the party admitted that Mr Vijay could have "worded the comment differently".
Mr Vijay was talking to al-Jazeera about attacks last month in Greater Noida, near Delhi, on a number of Nigerian nationals. Five Nigerian students were attacked by crowds, while another was beaten by a mob inside a shopping mall.
Police say five people have been arrested over the violence and India's Foreign Minister Sushma Swaraj has promised an "impartial" inquiry.
An Indian politician who said Indians were not racist because they lived alongside south Indians has sparked a strong response on social media.