Workers of local electoral commission branches in some areas demanded advance payment of their expense allowances worth $1.02 a day, delaying submission of voter registers from some areas until late on Thursday.
That would have given the Autonomous National Electoral Commission (CENA) just two days to print ballot papers and get them to polling stations across a country whose northern parts are a full day's drive away from the main Gulf of Guinea port city Cotonou.
A separate dispute within the top ranks of the CENA threw preparations into further chaos.
Election commissioners voted Antonin Akpinkoun, CENA chairman, out of the post on Tuesday, accusing him of disregarding a majority decision by awarding the contract to print ballot papers to a printing company favourable to Yayi, thereby increasing the potential for electoral fraud.
The Constitional Court then weighed in, upholding an appeal by Akpinkoun and reinstating him to the post, only for the CENA members to take another vote confirming his removal on Thursday, just three days ahead of the elections.
Previous elections have been tarnished with fraud claims and organisational problems since military ruler and former Marxist Mathieu Kerekou introduced multi-party democracy in 1991, although Benin has remained more peaceful than many nearby countries in volatile west Africa.
But a shooting attack on Yayi's convoy as he returned from an election campaign rally in the north of the country raised fears for the president's security.
Yayi said the attack was an assassination attempt by enemies opposed to his campaign to root out corruption.
A former head of the west African Development Bank whose election ended more than three decades rule by a political clique, Yayi has made fighting graft a cornerstone of his plan to revive Benin's lacklustre cotton-based economy.