Odili was elected governor of Rivers State in April 1999, and was reelected in April 2003. In September 2004, Amnesty International wrote an open letter to Odili expressing deep concerns for protection of human rights of civilians in and around Port Harcourt, detailing an increasingly alarming security situation in Rivers State, due to fighting allegedly between rival armed groups. In December 2004, a gang of armed youths believed to be members of the Egbesu cult attacked Odili's convoy along the East-West Road in Port Harcourt killing two people one a policeman In March 2009, the Rivers State Truth and Reconciliation Commission, headed by retired Supreme Court Justice Kayode Eso, blamed the crisis during Odili's period of office on both the state and the Federal Governments, particularly the administration of President Olusegun Obasanjo. The report outlined interwoven problems of failed governance, chieftaincy tussles, cultism, politics of acrimony and insurgency. During his governorship, Rivers State was in theory one of the wealthiest region in the country i.e. Lagos state, Delta state and Rivers State, due to oil and other business infrastructure, but Odili instituted relatively few improvements. In January 2007, the [Economic and Financial Crimes Commission under Nuhu Ribadu issued an interim report on the governor that pointed to severe implications of fraud, conspiracy, conversion of public funds, foreign exchange malpractice, money laundering, stealing and abuse of oath of office. At around the same time Human Rights Watch issued a report detailing pervasive patterns of corruption and mismanagement at the state and local levels under Odili's administration. In February 2007, Odili filed a suit challenging the powers of the EFCC to probe his administration in Rivers State. In November 2006, Odili announced that he would run for president in the 2007 election under the ruling PDP. However a day before the PDP's presidential primaries held on 16 December 2006, Odili stepped down from the contest, paving the way for another governor, Umaru Musa Yar'Adua, to emerge as the party's flag bearer.
Later career
In June 2008, Odili defended his record before the Rivers State Truth and Reconciliation Commission, denying the charges that had been made against him. As of December 2007, the office of Attorney General then headed by Michael Aondoakaa had refused to file any defense in court against Odili's claim that the EFCC was not authorized to investigate his administration. In March 2008, a Port Harcourt court ruled that the EFCC could not investigate state finances. In September 2009, a Federal High Court sitting in Abuja issued an interim injunction stopping the EFCC from arresting, detaining, prosecuting or embarrassing Odili over a N189m bank debt. However, a few days later the EFCC summoned Odili over alleged debts owed to five banks whose Managing Directors and board had recently been removed by the Central Bank of Nigeria. In December 2009, the New York Times published an article about the kidnapping industry in Africa. The author talked to a man called Adiele Nwaeze, who accused Odili of having paid him to help rig an election ten years ago by robbing ballot boxes. Odili denied the accusation. In September 2010, it was reported that former military head of stateIbrahim Babangida, who planned to be a candidate for president in the 2011 election, was in discussions with Odili over being his running mate as vice-presidential candidate. The choice was said to be due in part to a close relationship between Odili and Raymond Dokpesi, the director general of Babangida's campaign.