Faisal Juneja, Hanif Shaikh and Mohamad Mansuri have confessed to the crime, a senior crime branch official said.
The complainant had purchased a warehouse at Masjid Bunder from Faisal and Hanif in February, but had not got its possession, police said.
Faisal's father allegedly told the complainant that Chhota Shakeel, the fugitive gangster, had asked them not to give him the possession.
The complainant then asked Faisal and Hanif to return his money. The duo allegedly threatened him with dire consequences and said he would receive a call from Chhota Shakeel.
A few days ago, Faisal, Hanif and Mohamad went to the complainant's office and told him if he asked for his money again, he will have to pay Rs one crore or get killed by Chhota Shakeel.
Following a complaint registered at Azadnagar police station, the trio were arrested for extortion.