Police said 26-year-old Bamilola Kazim was allegedly assaulted by Mohammed Gafoor after a row on Wednesday
Mr Kazim was treated for wounds at a local hospital and released.
Last week a student from the Democratic Republic of Congo was beaten to death by a group of Indian men after an argument in Delhi.
Two men have been arrested in connection with the killing of the Congolese man.
Indian foreign ministry spokesperson Vikas Swarup  tweeted on Friday that Foreign Minister Sushma Swaraj "had urgently sought report" on Wednesday's incident from the local government "and is monitoring the case".
Police said Mr Kazim allegedly parked his car in front of Mr Gafoor's house, and was attacked with an iron rod by the latter after an altercation.
"We have arrested the accused and the matter is now in court," Hyderabad police officer K Krishnaiah told BBC Hindi's Imran Qureshi.
Gideon Omodowale of the local Nigerian Students Association said it was a "racial issue".
"If he was a US citizen or an Indian, he wouldn't have been attacked. Later, some community people came and he [Mr Gafoor] apologised. We are ready to drop the case because we don't want it to affect other Africans," he told the BBC.
There are more than 4,000 students from African countries in Hyderabad.
Following last week's killing of an African student in Delhi, a group of African embassies had said they did not want to participate in Africa Day celebrations on Thursday because of repeated attacks on African students in India.
They relented after Ms Swaraj promised to ensure the safety of African students in India.
Mr Swarup said the Indian government had received news from its embassy in Kinshasa, the capital of Democratic Republic of Congo, that some "Indian establishments and shops were attacked on 23 and 25 May as a reaction perhaps to the killing of the Congolese national" in Delhi.
"It has been reported that by Wednesday, things have calmed down," Mr Swarup was quoted as saying by The Hindu newspaper.
Authorities in the Democratic Republic of Congo have not yet commented on the remarks.
In February, a Tanzanian student was assaulted and partially stripped by a mob in the southern city of Bangalore.
India's foreign ministry says it is looking into an alleged attack on a Nigerian student by a local man in the southern city of Hyderabad.