The defectors have "embraced a narrow group of ethnic and religious bigots whose main intention is to unleash a state of anarchy on Nigeria," he said in a statement.
Jonathan's party has governed since decades of military dictatorship ended in 1999. He has not said he will run, but supporters already are campaigning.
Many northerners say Jonathan has broken an unwritten party pact to rotate the country's leadership between north and south to balance power in the fractious nation divided almost equally between Muslims and Christians. A Christian, Jonathan was vice president in 2010 when President Umar Yar'Adua, a Muslim, died in office. He took power and won 2011 elections.
Jonathan's government is considered by many to be largely ineffectual in dealing with the huge challenges confronting Africa's biggest oil producer and its most populous nation of more than 160 million.
An Islamic uprising has killed thousands in the northeast of the country. Neither Jonathan nor his officials have responded to charges that soldiers have committed gross human rights abuses and may have killed more people than the extremists.
Hundreds of people have been slain this year in ethnic-religious clashes over land and grazing rights across Nigeria's Middle Belt, where decades-old conflicts between mainly Christian farmers and largely Muslim nomadic herders has increased despite the deployment of security forces and peace committees.
While Jonathan's government has bought off militants whose attacks had scared off investment in the oil-rich Niger Delta, it has failed to curb thefts of oil estimated at 200,000 barrels a day 10 percent of production and a big chunk out of the national treasury. Military leaders and politicians are believed involved in the thefts, with only a small fraction stolen by locals aggrieved at the loss of farmland and fishing ground polluted by decades of careless oil production.
Nigeria's government is also seen as largely ineffective against rising piracy in its waters by criminals who have expanded their operations to neighboring countries in the Gulf of Guinea.
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Associated Press writer Bashir Adigun contributed to this report from Abuja, Nigeria.