According to police, Francis Taiwo is being investigated by the country's national anti-trafficking agency (Naptip) after admitting the treatment was a punishment, as his son was "possessed" and this had been leading him to steal.
Disturbing pictures have emerged which apparently show Pastor Taiwo's nine-year-old emaciated son in Ota, in the south-western state of Ogun, in chains.
A statement released by police said members of the 40-year-old's own congregation at the Key of Joy Celestial Church in Ogun assisted in the treatment.
He is accused of chaining the boy, who was rescued by the Nigeria Security and Civil Defence Corps (NSCDC), for more than a month.
Local police spokesperson, Muyiwa Adejobi, told the AFP news agency: "We reacted after a report that a boy had been trapped in a room near a church at Atan in Ogun State.
"We forced the door and we rescued him. He was in a very bad shape, very thin because he was malnourished. The boy said his father did not give him food regularly and had been locked in the room for more than a month"
It has also been reported Pastor Francis initially fled after the boy's rescue but was taken into custody along with his wife, the boy's stepmother.
The boy has received treatment and has been discharged from hospital.