"To describe people of Northeast living in Delhi as immigrants is not just a mistake, but an unpardonable insult," Gogoi tweeted.
He also attacked Prime Minister Narendra Modi of not taking the matter seriously.
"The PM has not viewed the matter seriously at all. This is really unfortunate," Gogoi said.
"It thoroughly exposes BJP's ignorance that NE is integral as any other part of the country," the Chief Minister said in a series of tweets on the microblogging site Twitter.
Even though the BJP apologised and came out with a rephrased version, the protests continued to rock various places of Assam.
Asom Yuba Parishad took out a rally in the city, while Youth Congress and NSUI protested and clashed with BJP workers in Silchar. Police, however, controlled the situation immediately.