By Alex Last
BBC News, Lagos
The head of the agency, Nuhu Ribadu, said Mr Ibori would be charged in the federal high court on Thursday.
Mr Ibori is also under investigation by the Metropolitan police in the UK.
The failure to prosecute Mr Ibori in Nigeria had raised doubts over the government's commitment to its anti-corruption campaign.
Mr Ibori is the most high-profile former governor to be arrested under the new administration.
Agents from Nigeria's Economic and Financial Crimes Commission (EFCC) arrested Mr Ibori at a private residence in the capital, Abuja.
Mr Ibori is the former governor of Delta State, one of the largest oil-producing states in Nigeria and, therefore, one of the richest.
But he has been under investigation in the UK over allegations he laundered millions of dollars of looted state funds - charges he denies.
A UK court has frozen assets in the UK, allegedly belonging to Mr Ibori worth $35m.
His official salary while in office was less than $25,000 a year.
Mr Ibori, like other state governors, lost his immunity from prosecution when he had to leave office earlier this year.
But the key political issue has been whether anti-corruption agencies would be allowed to go after him in the way they have gone after other former governors.
The actions of Nigeria's new attorney general have been under particular scrutiny in this case.
Law enforcement agents in the UK and Nigeria have complained that he has been using his position to stall the prosecution of Mr Ibori - a charge he denies.
Still, it raised questions as to the scope of the new president's anti-graft policy.
This arrest is a bold statement from the anti-corruption agency at least that no-one is safe from prosecution.