Ndubuisi Vitus Amaku said the resort state's subsequent order to deport Nigerians living illegally there was like "rubbing salt on their wounds".
Meanwhile, police in Goa have made the first arrest in the murder case.
Tensions have been rising since a Nigerian man was stabbed to death last week and five others were wounded.
Soon after the killing, nearly 200 Nigerians blocked Goa's main highway for several hours to protest against the killing, and police arrested 53 of the protesters.
Police blamed the killing on rivalry between local and Nigerian drug traffickers, and Goa's Chief Minister Manohar Parrikar asked the police to track down Nigerians living illegally in the state and deport them.
There are about 40,000 Nigerians living in India and Mr Amaku says he is concerned about the safety of his people.
"Indians need to understand that a large number of Nigerians are living legally in India and even if some are living illegally, there are laws in place to deal with that and those should be implemented," Mr Amaku told BBC Hindi's Divya Arya.
He criticised the Goan authorities for plans to deport those living illegally in India.
"If Nigerians are living illegally you don't wait till their compatriot is murdered before you go around picking them up and threatening them with deportation - that is like rubbing salt on their wounds."
Earlier in the week, another Nigerian diplomat had warned of repercussions against Indians living in Nigeria if Goa did not stop "evicting Nigerians" from the state and failed to arrest the killers.
More than 800,000 Indians live in Nigeria and they own approximately 100,000 businesses there.
Mr Amaku said the official's statement was made in the context of the murder and that he felt "aggrieved" like all other members of the Nigerian community.
Indian foreign ministry spokesman Syed Akbaruddin said he was sure that the row could be settled "amicably".
"We have been assured that the investigation (into the murder) is under way," news agency AFP quoted him as saying.
The Nigerian community in India is feeling "aggrieved" after one of its citizens was killed in Goa, Nigeria's high commissioner has told the BBC.