According to media reports, the NIA team took Arif, who had escaped from Iraq, into its custody at the Mumbai Airport.
Arif's relative Iftiqar Khan confirmed the development saying it was good news for the family that he had returned.
Yesterday, another Indian national Harjit Masih also escaped captivity after being held by ISIS militants.
Earlier on Friday, External Affairs Minister Sushma Swaraj had confirmed that Harjit was under the government's protection.
Swaraj had further stated that reports aired by a television channel, which suggested that the 40 Indians who went missing in Iraq in June had been killed by ISIS militants, were untrue and unfounded.
She also assured that the government is actively involved in locating the missing Indians. But she admitted that there was no proof whether the missing Indians were dead or alive.
Around 40 Indian nationals, who were employed by a construction company in Baghdad were kidnapped after Iraq's second largest city, Mosul, fell to the ISIS .