“There is fraud at the national level,” said former prime minister Sidya Toure after polls closed at 1800 GMT.
“We are seeing problems, especially concerning ink, in a lot of polling stations,” added Toure, who heads the opposition Union of Republican Forces (UFR).
The local elections are the first since the end of the era of military dictatorship and follow eight years of delays blamed on a lack of funds, political infighting and the 2013-16 Ebola crisis.
People chose among nearly 30,000 candidates for councillors, including 7,000 women, across the mineral-rich but deeply poor former French colony.
The campaign largely focused on failing schools, high unemployment, electricity shortages and corruption allegations.
After casting his vote, President Alpha Conde told his supporters: “We do not want fraud and if that happens, we will have to resist as we have always done.”
But Toure and other opposition figures criticised the polling.
“We will demonstrate that President Alpha Conde has, with the help of the administration, stolen this election, which will not benefit him,” said another former prime minister, Cellou Dalein Diallo, leader of the opposition Union of Democratic Forces of Guinea (UFDG).
The last local election was held in 2005 under the decades-long rule of authoritarian leader General Lansane Conte, who died in 2008.
The military then took control until the presidential election of Conde in 2010.
Despite the ushering in of civilian rule, the local elections were repeatedly postponed and Sunday was the first time that many councillors, controversially appointed by Conde, were facing the ballot box.
“This is the first time I have voted for a mayor. I hope my candidate wins and puts in place his programme to clean up our district, create employment and make our city safe,” said taxi driver Simbaya Aboulaye Soumah in the capital Conakry.
In Simbaya, a Conakry suburb, eager voters lined up at a polling station at a primary school an hour before polls officially opened at 0800 GMT.
“We want change for the youth because if you look for the development of a people, a nation, it is via the youth,” said Mohamed Toure, a student.
“We want them (councillors) to help the young people,” he added.
Sixty percent of Guinea’s population are aged 25 and under, and their memories of military rule and life under authoritarian Conte are either hazy or non-existent.
Political distrust is high in Guinea, where ethnic tensions often turn deadly around election time.
More than 5.9 million Guineans were registered to vote.