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Lamido Sanusi has spearheaded reforms in Nigeria's troubled banking sector since his appointment in 2009
Nigeria's state oil firm has denied failing to account for the money, saying the claim was "unsubstantiated".
Mr Sanusi is widely respected after undertaking reforms to the banking sector since his appointment in 2009.
He was named central bank governor of the year in 2010 by Banker magazine.
Nigeria is one of the world's biggest oil producers but the sector is marred by widespread allegations of theft and corruption.
Anti-corruption credibility In February, Mr Sanusi told a senate committee that out of $67bn of oil sold between January 2012 and July 2013, $20bn had not been accounted for.
The Nigerian National Petroleum Corporation said the allegations showed "little understanding of the technicalities of the oil industry".
Mr Sanusi is currently in Niger attending a meeting of regional central bank heads.
He is to be replaced by his deputy, Sarah Alade, who is travelling with him.
President Jonathan asked him to resign in December but Mr Sanusi refused, sources told the BBC Hausa service.
The president does not have the power to sack the central bank governor - only the National Assembly can do this.
His term in office was due to end in June but correspondents say the decision to suspend him now is still very significant.
The presidential statement announcing his suspension said he had been removed pending "investigations into breaches of enabling laws, due process and mandate" of the Central Bank of Nigeria.
BBC Abuja editor Bashir Saad Abdullahi says news of his suspension could further damage the anti-corruption credibility of President Jonathan's administration.
Nigeria central bank head Lamido Sanusi ousted
Lamido Sanusi has spearheaded reforms in Nigeria's troubled banking sector since his appointment in 2009
Nigeria's
central bank governor Lamido Sanusi has been suspended by the president
pending investigations into "far-reaching irregularities".
Mr Sanusi caused shockwaves in Nigeria when he alleged that $20bn (£12bn) in oil revenue had gone missing.Nigeria's state oil firm has denied failing to account for the money, saying the claim was "unsubstantiated".
Mr Sanusi is widely respected after undertaking reforms to the banking sector since his appointment in 2009.
He was named central bank governor of the year in 2010 by Banker magazine.
Nigeria is one of the world's biggest oil producers but the sector is marred by widespread allegations of theft and corruption.
Anti-corruption credibility In February, Mr Sanusi told a senate committee that out of $67bn of oil sold between January 2012 and July 2013, $20bn had not been accounted for.
The Nigerian National Petroleum Corporation said the allegations showed "little understanding of the technicalities of the oil industry".
Mr Sanusi is currently in Niger attending a meeting of regional central bank heads.
He is to be replaced by his deputy, Sarah Alade, who is travelling with him.
President Jonathan asked him to resign in December but Mr Sanusi refused, sources told the BBC Hausa service.
The president does not have the power to sack the central bank governor - only the National Assembly can do this.
His term in office was due to end in June but correspondents say the decision to suspend him now is still very significant.
The presidential statement announcing his suspension said he had been removed pending "investigations into breaches of enabling laws, due process and mandate" of the Central Bank of Nigeria.
BBC Abuja editor Bashir Saad Abdullahi says news of his suspension could further damage the anti-corruption credibility of President Jonathan's administration.