The pastor caused a stir when he mounted the pulpit carrying a gun.
The Federal Capital Territory Police Command has arrested Pastor Uche Aigbe of the House on the Rock church, Abuja, according to an official statement.
The statement signed by Josephine Adeh, FCT Police Public Relations Officer, said the police acted on intelligence to arrest Mr Aigbe and two others on Monday.
The cleric, who is a pastor of the church, caused a stir on Sunday when he mounted the pulpit carrying a gun.
The incident took place during the second service, which frequently has a high turnout of the congregation, the Punch newspaper reports.
Pictures of Mr Aigbe holding the AK 47 rifle have gone viral on the internet with social media commentators raising concern about the cleric's action.
"The pastor's message and demonstrations were tagged inciting by various media and social media users," the police statement read, adding, "The Church Chief Security Officer and one Inspector Musa Audu were also arrested."
The police also confirmed that Mr Audu was on duty on the said day and he "unprofessionally released his rifle to the said pastor without permission or recourse to police authority."
Discrete investigation has commenced, the police added, urging members of the public to shun actions or utterances that are in breach of extant laws.
"The law is trite and all violators will be adequately sanctioned," the police said.
Pastor's action is regrettable
Earlier in a statement on Monday evening, the House on the Rock church said Mr Aigbe carried the gun to illustrate his message to the congregation not to incite violence.
The statement said: "On Sunday, February 12, a resident pastor of House on the Rock, Abuja Church, Pastor Uche Aigbe in a message about fighting the good fight with spiritual weapons, carried an unloaded gun to illustrate his message on 'Guarding your Faith.
"Pastor Uche has been a leader in House on the Rock, Abuja since 1999 and has always shown exemplary leadership. However, he realises that even with the best of intentions, carrying a gun to illustrate his message was ill-advised and regrettable."
Without hesitation, the church said, Mr Uche acknowledged the gravity of his actions and apologised unreservedly for them.
"As a church, House on the Rock rejects all forms of violence and we stand on the good news gospel of Jesus Christ which embraces peace and goodwill for all of mankind.
"We are cooperating fully with the authorities as they carry out their investigations into this incident, and we will continue to engage internally to ensure this break in protocol does not happen again," the statement said.