Sowore was arrested at his house in Lagos and moved to area F at Ikeja on Wednesday after Fatodu, lodged complaint to police.
The Police got a tip off that Sowore was in the state and stormed his house for his immediate arrest.
Mr. Fatodu posted a tweet saying he “just got Sowore Omoyele of Saharareporters arrested for criminal defamation and blackmail and threat to my life and career.”
Mr. Sowore said Mr. Fatodu attacked him after he drove out of a restaurant situated along Isaac John Street.
“I went with a friend to have lunch in a restaurant and as we drove out of the place we got on Isaac John Street,” Mr. Sowore said. “After driving for a few minutes, I slowed down by a construction site on the road and someone knocked on my window.”
Mr. Sowore said he immediately recognised Mr. Fatodu and wound down to greet him only to be physically attacked and dragged out of his vehicle.
“The construction workers and other people around moved closer to intervene and the police were called in,” he said.
The police took Mr. Sowore, Mr. Fatodu and others involved in the incident to Area “F” Command Headquarters, also in Ikeja.
It was here that the Commissioner of Police, Fatai Owoseni, said Mr. Sowore should be transferred to the State Criminal Investigation Department in Panti, Yaba, Lagos.
“It is unfortunate that the commissioner will treat such a brutal attack against me this way,” Mr. Sowore said.
“The matter that was before him was only about the immediate threat to my life only for him to further endanger my life by asking them to send me to Panti.”
Dolapo Badmus, the police spokesperson in the state, said Mr. Sowore was sent to Panti based on a petition against him.
Mr. Badmus said the petition was filed by Mr. Fatodu and it involved criminal defamation, blackmail and threat to life.
“The commissioner received the petition yesterday and he immediately referred it to Panti for further investigation,” Ms. Badmus said. “That is why he was driven there for further investigation in his case.”
Ms. Badmus could not immediately say if or when Mr. Sowore would be arraigned before a court.
“The matter is still under investigation,” she said.
Mr. Sowore founded Sahara Reporters in 2006 to promote citizen journalism by encouraging everyday people to report stories about corruption, human rights abuses and other political misconduct in Nigeria.
A story the platform published in January 2016 alleged that Mr. Fatodu stood as front for a former Minister of Aviation, Femi Fani-Kayode, in the mismanagement of funds meant for the purchase of arms for the military.
Mr. Sowore said he believed Mr. Fatodu’s attack against him was “strictly because of the report and other numerous investigations of Sahara Reporters against him and his benefactors.”
Mr. Fani-Kayode is currently standing trial on allegations that he received funds from a former National Security Adviser, Sambo Dasuki.