Obasanjo said his government only arrested and investigated Bamaiyi over allegations that he killed some people during Abacha's reign.
The ex-president said that under his administration between 1999 and 2007, Bamaiyi was arrested and investigated over allegations against him that he killed some people during the reign of military dictator, Gen. Sani Abacha.
He said it was only on this ground that the law enforcement agencies in the country prosecuted him.
The elder statesman stated this on Sunday, April 9, at his Presidential Hilltop residence in Abeokuta, the Ogun State capital while hosting members of the Ogun State Correspondents' chapel.
In Bamaiyi's recent book, 'Vindication of A General', he accused Obasanjo of plotting to kill him so that any plan by the former army chief to overthrow him would be buried.
According to Bamaiyi, Abdulsalami Abubakar had suggested to Obasanjo to cage him because of his (Bamaiyi) capability of toppling the new administration.
In the book, Bamaiyi stated, "Upon handing over power to Gen. Obasanjo in May 1999, Gen. (Abdulsalami) Abubakar told the new civilian President that he must rein in General Bamaiyi, else, he would overthrow the new government and from that moment, General Aliyu Gusau, the then National Security Adviser, and President Obasanjo made it a duty to imprison me by all means.
"When Obasanjo took over, some Peoples Democratic Party big shots decided that based on the report, I had control of the Army and should be arrested. The government looked for avenues to arrest me.
"They started by checking Army accounts to see if I had stolen money."
Reacting to the allegations, Obasanjo, who was said to be visibly angry, denied any plot by his government to kill Bamaiyi, but admitted his regime arrested him to ensure that he answered for his misdeeds.
Obasanjo said: "That I wanted to kill him? What of the people he allegedly killed? My government did not plot to kill him. My government asked him to answer for those that were alleged to have been killed by him and that is legitimate.
"That is if there is an allegation that you have done something, that you have committed a crime, then you are arrested; you should answer. That’s all; pure and simple!
"Who the hell is he that I would want to kill him? Kill him for what? To achieve what? No! There were allegations, the police and the law enforcement agencies decided to look into the allegations.
"They invited him and they asked him to answer as a result of what was found, so they charged him to court. So, it’s now up to him, the investigators, as I said, the prosecutors and the judiciary. That’s all."
In the book, Bamaiyi also revealed that late politician and business mogul, MKO Abiola did not die of natural causes, challenging Abdulsalami Abubakar to unveil the real truth.
Abiola was arrested by Gen. Abacha in 1994, after Gen. Ibrahim Babangida annulled the election which he purportedly won in 1993.