Footage circulating on social media showed Abdulrahman Ibrahim, a consular officer based in Jakarta, being held down in a vehicle by several men.
Nigeria called it "an egregious act of international delinquency by the Indonesian state".
It vowed to review bilateral relations with the south-east Asian nation.
The video showed one of the officials putting his hand on the diplomat's head and pushing it back against a seat.
Between yells of protest, Mr Ibrahim repeated: "I can't breathe."
Later in the one-minute-and-30-second clip Mr Ibrahim was heard saying: "My neck, my neck."
Mr Ibrahim had been detained on a street in the Indonesian capital, Jakarta.
The incident has caused anger in Nigeria, with many saying it shows the disdain that other countries hold for Nigerians. Some are calling for a full explanation from the Indonesian government.
Nigeria's foreign ministry had previously sent a letter of protest to the Indonesian government saying the mistreatment Mr Ibrahim endured was "against international law and the Vienna Conventions governing diplomatic and consular relations between states".
Indonesia's envoy to Nigeria was also summoned on Monday over the incident and apologised on behalf of his government, the foreign ministry said.
Immigration officials had also apologised to Nigeria's ambassador to Indonesia, it added.
Meanwhile Nigeria's ambassador in Jakarta has been called home to give a full report to the government, and the foreign ministry says consultations will continue.
By Chris Ewokor