Guinea’s run-off poll due on Sunday is in doubt after the new electoral head found serious logistical shortfalls.
Key materials have not been distributed, while computers used for vote-counting have been stolen.
Gen Toumany Sangare, who only took over at the electoral commission a day ago, is set to meet the two presidential candidates later on Friday.
The election is intended to be the country’s first democratic poll, after 52 years of authoritarian rule.
The military seized power in 2008, leading to two years of political upheaval.
After meeting the two candidates, Gen Sangare will take a decision on whether to go ahead with the vote that has been twice delayed, causing street clashes.
The BBC’s Alhassan Sillah in the capital, Conakry, says just 24 hours into his new job, Gen Sangare is beginning to realise that the task ahead of him is bound to stretch his much-heralded experience in the management of elections.
The Malian national was appointed by the military leader after months of infighting and accusations of fraud at Guinea’s electoral commission.
During Thursday’s meetings at the commission, Gen Sangare discovered that neither the alpha-numeric voter cards nor the sealed voter envelopes have been distributed.
It was also revealed that computers meant for electronic vote-counting were stolen from the commission’s premises earlier this week.
Meanwhile, agents and other temporary electoral staff have threatened to boycott the vote if salary arrears going back 11 months are not paid.
Gen Sangare also met interim Prime Minister Jean-Marie Dore, who urged the new electoral chief to tread carefully as he feared further violence.
The country has been tense since the first round vote in June and the run-off has been delayed – once in July because of investigations into electoral fraud and again in September because of clashes between rival supporters.
Alpha Conde (l)
Age: 72Long-time opposition leaderJailed several times18% of first-round votes
Cellou Dalein Diallo (r)
Age: 58Minister 1996-2004Prime minister 2004-644% of first-round votes
Earlier this week, two supporters of Cellou Dalein Diallo were killed as police opened fire on crowds demanding the removal of the former election commission head who they accused of bias.
Both presidential candidates, Mr Diallo and Alpha Conde, have given their backing to Gen Sangare.
Meanwhile, diplomatic sources confirmed to the BBC that troops from neighbouring Sierra Leone have been deployed to patrol the area near their common border.
A former prime minister, Mr Diallo is seen as the favourite to win the run-off. He took 44% of the votes in the first round – and claims he was denied overall victory only by fraud.
Mr Conde, a veteran opposition leader, won 18% of the vote – although he claims he was cheated out of some 600,000 ballots.
Correspondents say the fierce tensions between the two candidates’ supporters has its origins in rivalry between Guinea’s two largest ethnic communities. Mr Diallo is a Peul, while Mr Conde is a Malinke.
Despite their economic dominance, a member of the Peul community has never been president. The Malinke are heavily represented in the ruling military junta.
The first round was seen as Guinea’s first democratic vote since independence in 1958, raising hopes of an end to military and authoritarian rule in the mineral-rich country.
Guinea is the world’s largest exporter of the aluminium ore bauxite. It also has important deposits of iron ore, but it remains one of the poorest countries in West Africa.
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