He commended Nigerians for achieving a measure of success in nation-building despite what he called "occasional appearances to the contrary."
However, he said, recent troubles in Nigeria -- armed revolt, economic disparity and corruption -- had inflicted spiritual damage to the nation, making it difficult to live together as children of God.
Archbishop Onaiyekan also urged Nigeria's leadership to live up to its responsibility by restoring and maintaining security in the land and by bringing opposing forces together for dialogue and reconciliation.
"Especially, the civil authorities must continue the efforts to disarm violent aggressors who attack and kill innocent people," he said.
Boko Haram, an extremist Islamic sect with somewhat undefined leadership and goals, has targeted Nigerian leaders and public institutions with increasing violence since 2009. The Associated Press reports that, in the first two months of 2012, the sect was blamed for killing at least 310 people.
Archbishop Onaiyekan said no amount of grievances about impoverishment, marginalization or neglect can justify attacks on and destruction of innocent human lives and hard-earned property.
Freedom of religion means respect for all, the archbishop said.
"It is about time, therefore, that we sincerely examine our attitudes and review certain practices of religious intolerance, some of which have been inherited from earlier times," he said.
He called on Christians to undergo a continuous spiritual transformation by acknowledging their sins, repenting and forgiving others.
Much damage has been done under the guise of religious fanaticism, the archbishop said.
"Life and properties have been wantonly destroyed. Our social life has been seriously dislocated as refugees are moving up and down in the byways and highways of our nation," he said.
"Over and above all, the image of our nation has been seriously dented abroad," he added.