2 February 2014 Last updated at 21:12 ET 
The current vice-president has more than 49% of the votes, but is still short of the 50% plus one needed to avoid a run-off election.
Trailing more than ten points behind is the right-wing opposition candidate Norman Quijano, from the Arena party.
Former President Antonio Saca, is trailing with 11%.
The campaign has been dominated by the sluggish economy and gang crime.
El Salvador’s murder rate is among the highest in the world.
Correspondents say there are signs that a recent truce agreed between the two main street gangs is falling apart.
Mr Sanchez Ceren. 69, was a rebel commander when the Farabundo Marti National Liberation Front (FMLN) was a guerrilla group during the 1980-1992 civil war.
He has promised to tackle crime through education and social programmes.
Candidates have clashed on how to deal with gangs, as Will Grant reportsOpinion polls suggest he had a lead over Mr Quijano, who stood down from his position of mayor of San Salvador to stand for president.
Many voters are critical of the 2012 truce with gangs, and Mr Quijano has accused the administration of outgoing President Mauricio Funes of negotiating with criminals. He is advocating tougher policies against drug gangs.
The truce has led to a decrease in El Salvador’s murder rate, but gradually the number of killings is going back up.
The three-way race may lead to a run-off vote Analysts say the vote may hinge on the popularity of the third candidate, former President Antonio Saca who is running for the new Unidad party.
The second round of voting, if needed, is to be held on 9 March.
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El Salvador vote counting under way
