Agagu was appointed by President
Olusegun Obasanjo as his first minister of Aviation in 1999.
In September 2008 a Senate Ad-Hoc Committee investigating the Transportation Sector summoned Agagu and others as part of its probe of the entire transportation sector, to answer questions about his tenure as Minister of Aviation.
[6] On 5 March 2009 Agagu was questioned by the EFCC for Alleged N25Bn spent on OSOPADEC during his administration, while the new administration led by Governor Olusegun Mimiko also commenced probe of contracts awarded in the last six months of his administration.
He died on Friday 13, Sept 2013 in Lagos. On 3rd of October 2013, a day before his burial the plane,
Associated Aviation Flight 361 carrying his corpse together with 13 passengers and 7 crew members crashed in Lagos.