At one location in southern Brazzaville as few as 52 of 924 registered voters reportedly cast their ballots.
However, the country's electoral commission gave a vastly different version of events, telling AFP after the polls had closed that turnout had been "massive" in parts of the country.
"We cannot speak of fraud when we had 170 international observers on the ground"
Alain Akouala Atipault, Congo communications minister
In a statement opponents of Sassou-Nguesso called on "national and international opinion to acknowledge the illegitimacy" of the vote and demanded "a new presidential ballot organised with the agreement of all political forces in the country".
Provisional results from the election are expected later this week, with the possibility of a second round if no candidate wins more than half the vote.
In their statement, the opposition candidates said an overwhelming majority of the electorate had shunned Sunday's ballot.
"The Congolese people have clearly expressed themselves with this record abstention of more than 90 per cent," said the statement, alleging massive rigging and vote-buying.
"By this strong rate of abstention, the Congolese who love justice and peace have expressed their rejection of this totalitarian, arrogant and corrupt regime."
The Congolese government rejected the charge, saying the opposition declarations of massive fraud are "incorrect and do not hold".
"We cannot speak of fraud when we had 170 international observers on the ground," Alain Akouala Atipault, the communications minister and government spokesman, said.
Sassou-Nguesso has ruled Congo for almost a quarter of a century, losing multiparty elections in 1992 before coming back to power in a civil war that destroyed much of the capital in 1997.
The president won the last election in 2002, when his main rivals were banned or withdrew, citing irregularities.
Despite an abundance of oil and timber – its principal exports – 70 per cent of Congo's inhabitants still live below the poverty line.