Allegedly using a racially insulting term, Naik said, "The government of India should ban them (Nigerians)."
"They should be probed and it should be checked whether many of them are here to study or for picnics or to sell drugs," Naik said, adding they "create trouble" in the country.
The Congress leader, during a press meet, alleged that Nigerian nationals stay in the country and "indulge in illegal activities".
He also demanded that the "bogus" educational institutes, which give them admission, should be probed by the law enforcement agencies.
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The Congress leader's controversial statements comes days after similar remarks about the Nigerian nationals made by Goa Chief Minister Laxmikant Parsekar and his Cabinet colleague Dilip Parulekar.
Parsekar had termed Nigerians as "annoying" and having "different attitude". He had later said that his statement was distorted and taken out of context by a section of media.
The comments by Parsekar and Parulekar, both of BJP, were made in the wake of attacks on Africans in New Delhi last month.