Goa's art and culture minister Dayanand Mandrekar on Thursday apologised for calling Nigerians a "cancer".
Mandrekar had made the statement after around 200 Nigerians rioted and blocked a major highway in the state last week to protest the murder of a Nigerian man in Mapusa in south Goa.
"It's my mistake to make such statement. I apologise," Mandrekar told reporters at Panaji.
On Sunday, the minister told the Press Trust of India (PTI) that Nigerians were like a "cancer" and their actions were detrimental to the tourism industry.
However, he insisted that what the Nigerians did in Goa was wrong.
The protesters had clashed with police and locals, and more than 50 Nigerians were arrested.
Chief minister Manohar Parrikar then ordered police to identify Nigerians who were illegal residents of the state and said they must be deported.
Parrikar also accused a Nigerian diplomat of sending "offensive SMSes" to a senior police officer over the murder of the Nigerian national.
"He (the diplomat) was wrongly briefed and went to the extent of sending offensive SMSes to our superintendent of police," Parrikar told reporters at Vasco town on Thursday.
The chief minister did name the diplomat, who was recently in Goa.
The diplomat had reportedly warned of "repercussions" against Indians living in Nigeria if his fellow countrymen were harassed in Goa.
The murder and protests have also sparked a diplomacy row with the African nation.
Nigeria had earlier issued a note verbale to India conveying concerns over the security of its nationals and demanded immediate arrest of those who killed the Nigerian man. The Indian government assured Nigeria that all issues would be addressed in a cooperative manner.
Police have arrested one person in connection with the murder.
(With inputs from PTI)
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