With just under 94 percent of ballots counted from Sunday's election, leftist ruling party candidate Lenin Moreno had just over 39 percent of the vote, according to the National Electoral Council.
That was just short of the 40 percent needed to avoid a runoff against his conservative rival Guillermo Lasso, who was on 28.4 percent.
The president of the National Electoral Council, Juan Pablo Pozo, said it could take until Thursday for the full results to be confirmed.
"That it should take three days to publish final results is an attempt at fraud and we are not going to allow that," he wrote on Twitter.
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The electoral council has denied any fraud took place. It insisted in a statement that it would "guarantee that the people's will is respected."
"Never in the history of the country have results come out less than 48 hours after the end of voting," it said on Twitter.
Supporters of Lasso earlier scuffled with police as they gathered outside the electoral council, impatient at the delay.
Political analyst Santiago Basabe of the social science institute FLACSO said it was "difficult for the current trend (towards a runoff vote) to be reversed."
Opinion polls indicate Moreno may well lose a runoff in which supporters of other conservative opposition groups are likely to rally behind Lasso.
Sunday's election was a test of the legacy of outgoing President Rafael Correa, Moreno's more hardline ally, who is an outspoken critic of the United States.
Ecuadorans voted on whether to continue Correa's tax-and-spend policies or give Lasso a mandate to cut spending and taxes.
Lasso has also said he will consider ending WikiLeaks founder Julian Assange's asylum in Ecuador's London embassy.