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Bayelsa State Governor Diepreye Alamieyeseigha was arrested in London in September 2005 after investigators found roughly £1.8 million in cash at his residence and uncovered London properties allegedly bought with laundered state funds.

Alamieyeseigha jumped bail in December 2005, reportedly fleeing the UK disguised as a woman, and returned to Nigeria. The Bayelsa State House of Assembly impeached him that same month. He was subsequently prosecuted by the EFCC and pleaded guilty to corruption charges in July 2007, receiving a token sentence relative to the scale of the allegations.

As Vice President and chairman of the Petroleum Technology Development Fund (PTDF), Atiku Abubakar was accused by allies of Obasanjo of diverting PTDF funds and scholarships for personal or political benefit, allegations that surfaced prominently amid the 2006 dispute over Obasanjo's third-term bid, which Atiku had publicly opposed.

A panel investigation and EFCC scrutiny followed, and the administration attempted to use the allegations to block Atiku's eligibility to contest the 2007 election. The Supreme Court ultimately ruled in February 2007 that he could not be excluded from the ballot, and no criminal conviction resulted from the PTDF allegations.

Inspector-General of Police Tafa Balogun was accused of diverting roughly ₦17 billion in police funds — including money meant for police equipment and welfare — into personal accounts and businesses over his tenure.

Balogun was removed from office and prosecuted, pleading guilty in November 2005 to a reduced set of money laundering charges. He was sentenced to six months in prison and ordered to forfeit assets — a real conviction, though a lighter sentence than the scale of the alleged theft suggested.

The National Integrated Power Project, launched in 2005, was found in later National Assembly reviews to have spent an estimated $10-16 billion on new power plants and infrastructure with little corresponding increase in electricity delivered to consumers, raising allegations of inflated contracts and weak oversight.

The bulk of the scrutiny and formal probes into NIPP spending occurred under successive administrations rather than during Obasanjo's own term, and no comprehensive independent audit or prosecution was concluded regarding the funds spent while he was in office.

Repeated fuel price increases and periodic scarcity through the term were linked by labour unions and civil society to allegations of racketeering in fuel importation and subsidy claims, with marketers and officials accused of exploiting price gaps and import licensing for personal gain.

No comprehensive independent investigation into fuel importation racketeering during this period was concluded, and the underlying vulnerabilities in subsidy administration persisted well beyond the term, becoming the subject of a much larger scandal under the following administration.

Education Minister Fabian Osuji was accused of authorising a ₦55 million bribe to Senate President Adolphus Wabara and other National Assembly leaders to secure a favourable education budget allocation in 2004-2005.

Wabara resigned as Senate President in March 2005 and Osuji was sacked as minister, but neither faced a swift criminal conviction during Obasanjo's remaining time in office. Osuji was eventually convicted years later, in 2012, for his role in the scandal — an outcome well outside the administration in which the bribery occurred.

The 2003 award of 24 marginal oil fields to indigenous companies — intended to boost local participation in the oil sector — was alleged by civil society and industry observers to have involved politically connected beneficiaries with limited technical or financial capacity to develop the fields, raising questions about the transparency of the selection process.

Several of the awarded fields remained undeveloped or underdeveloped for years, and no comprehensive public investigation into the original allocation process was concluded during the remainder of the term.

Beyond the Wabara-Osuji case, broader allegations circulated within the National Assembly of the 2004 and 2005 federal budgets being padded with self-serving allocations by legislative leadership, echoing complaints that would recur in subsequent administrations.

No comprehensive independent investigation or prosecution of the wider padding allegations was concluded, and the National Assembly did not publish a full accounting of the disputed allocations.

As chairman of the Nigerian Ports Authority board from 2001 to 2003, Bode George was later found to have presided over contract splitting and inflation schemes worth an estimated ₦84 billion, structuring large contracts into smaller pieces to evade due-process approval thresholds.

The bulk of the investigation and prosecution occurred years after Obasanjo left office — George was eventually convicted in 2009 — meaning no accountability had been secured for the underlying conduct by the end of the administration in which it occurred.