Burkina Faso President Roch Kabore edged closer to re-election on Wednesday amid opposition concerns over the validity of the count, extending a commanding lead over his rivals with over half of districts reporting results.

Results posted to the election commission website on Wednesday morning showed Kabore with over 593 000 votes, almost four times as many as his nearest rival, former finance minister Zephirin Diabre.

Having secured 58% of total ballots cast, Kabore is on track to secure enough votes to avoid a second round.

Opposition uncertainty over the count complicates an election already troubled by threats from Islamist militants. Hundreds of thousands of citizens were unable to cast ballots on Sunday because their polling stations were closed for fear of violence.

On Tuesday the election commission resumed announcing results district by district after a more than 24-hour pause caused by opposition objections.

Five opposition representatives in the 15-member commission temporarily suspended their work on Monday afternoon over concerns that some districts had not produced manual vote tallies to accompany electronic tallies, as required by law.

On Wednesday they resumed work, but questioned the validation of results that had resumed without their oversight.

"Public opinion and political actors will judge the scope and validity of such validations and proclamations," the five opposition members of the 15-person commission said in a statement.

On Sunday polling stations were closed across swathes of the north and east where groups linked to al Qaeda and Islamic State operate. Some that had planned to open were shut because of threats.

Kabore, who won election in 2015, has said the vote went smoothly. The 63-year-old president campaigned on achievements such as free healthcare for children under the age of five and vowed to do more to address rising insecurity.