He announced a "national dialogue" to heal rifts and urged unity to avoid the fate of Syria. Nigeria suffered a civil war in the late 1960s that killed up to a million people.
Jonathan spoke from Aso Rock, the presidential villa that overlooks the central capital, Abuja, which three years ago was rocked by twin bomb attacks at a stadium where Jonathan and other officials were celebrating independence day in 2010. Twelve people were killed and 17 wounded in the attack claimed by militants from the Niger Delta fighting to end injustice in southern oil-producing states where people remain impoverished while foreign oil companies and government officials enrich themselves.
Since then, Jonathan has marked independence from inside his well-guarded presidential compound, where he released white doves Tuesday in a traditional sign of peace.
A helicopter made reconnaissance flights over Abuja, where police were on a red alert. Celebrations took place across the country with no immediate reports of disturbances while police and security forces deployed in a heightened state of alert.
The government negotiated an end to the Niger Delta insurgency in 2009 and paid off top rebel leaders. But the mass thefts of oil started by the militants continue to threaten the economy, with an estimated 200,000 barrels a day 10 percent of production siphoned off pipelines.
Analysts suggest similar negotiations could help end the uprising led by the Boko Haram terrorist network the name means "Western education is forbidden" which appeals to some of the millions of unemployed and ill-educated Muslim youths who feel marginalized by a government accused of massive corruption and bad governance. Boko Haram aims to overturn democracy, install an Islamic state and allow only Islamic schools in Nigeria.
Jonathan on Saturday likened the threat from Boko Haram to oil thefts, saying both are cancers that must be crushed.
In a message marking the anniversary, the United States said it "stands with all Nigerians to reject the heinous violence that continues to be perpetrated by Boko Haram and other extremist groups" and urged the government to bring the perpetrators to justice and to protect civilians.
Violence has continued unabated across central Nigeria, where deadly fights regularly erupt over politics, business, land and water rights, religion and other issues. Police said at least 11 people were killed and several homes torched Saturday in an ongoing fighting over grazing land between nomadic cattle herders and farmers. It was the seventh attack in five months on Zangang village, Kaduna state, in a conflict that began after farmers whose crops were destroyed by cattle killed two cows.
Local elders say increasing numbers of nomads are moving south and west as they flee the violence in the northeast.
Jonathan condoled with the families of victims of terrorism and vowed to spare no cost "in the quest to enable our people live without fear."
In one positive development, the government this week handed over the much-hated state power utility to 14 buyers, a privatization move some hope will end chronic power shortages that cripple industry and inflate prices because of the high costs of running generators on diesel.
Many Nigerians remain cynical. "Until we see the power" no one will believe it, civil servant Idris Yusuf said in Abuja. "We have had so many promises over the years, nothing yet has come to fruition."
Jonathan is personally challenged by an internal power struggle in his party and a newly formed coalition of opposition parties as the country gears up for 2015 elections. That campaign is being tainted by religious and regional rivalries with many northern Muslim governors opposed to the candidature of Jonathan, a Christian from the south. The president has sidestepped questions about whether he will run again.
Internal rivalries threaten the continued dominance of Jonathan's party, which has won every election since decades of military dictatorship ended in 1999.
