Polling stations opened late and voter registers and ballot papers were not available in many polling stations, observers from the African Union and Economic Community of Central African States said in a statement.
According to local observers, the polls were marred by poor organisation and most polling stations opened long after 7am.
"In Talangaï area, north of the capital, no polling centre opened before 3pm because of delays in the distribution of electoral materials," said Quentin Banga, an observer from a civil society group known by its French acronym, CAPE. The group deployed 40 observers throughout the country.
The elections, on 24 June, were held to choose 137 deputies for the National Assembly. "The situation was chaotic," said Augustin Dimi Gueko, another CAPE observer.
In Impfondo, capital of Likouala region, voters kept moving from one polling centre to another searching for their names. Many could not find themselves on the voters' roll.
Henri Bouka, head of the national electoral commission (known by its French acronym, CONEL) admitted some problems were encountered during the elections, but said local administrations had not made proper arrangements - a view supported by one of his deputies in Pointe Noir.
The commission members are nominated by the president - one of the concerns raised by the many political parties that boycotted the poll, believing the commission would only serve to entrench President Dennis Sassou-Nguesso's 23-year-old hold on power.
But the president, talking to reporters after casting his ballot in Brazzaville, urged people not to pass judgment until the election results were published.
The level of disorganisation was worse than in previous elections, observers said. "I saw people going to [several] polling centres before they could find their name; others looked in vain," Serge Thierry Vedze Batonga, a journalist working for Radio Moka in Impfondo, said.
An angry woman at Omar in Impfondo claimed the situation was designed to suit certain candidates. "It was done for a reason," she said. "The organisers had to get rid of some names because they don't want the candidate for whom we are willing to vote."
There were similar problems in the Pool region in the southeast where the 2002 elections could not be held in some of the 14 electoral areas because of fighting between the rebels of Pastor Frédéric Bintsangou, alias Pastor Ntoumi, and government troops.
Pastor Ntoumi renounced violence in June and vowed to work for the strengthening of peace and democracy, and stood for election in Kimba constituency on the ticket of his Conseil National des Républicains (CNR) party.
According to local observers, no census had been conducted in the Pool, which led to many voters not being registered. Instead, their names were added manually to voter lists - which angered voters in Mossendjo and Mayoko in Niari department, Djambala in Plateaux and Liranga in Likouala.
In Liranga, locals said many of their names were not on the voters' roll and in some instances the names of children were listed instead.
Next time, plan better
For several days before the poll boycott was announced, the parties had questioned the organisation of the elections and denounced the electoral commission.
Roger Bouka Owoko, one of the observers and head of Congo's human rights organisation, deplored the chaotic setting of the elections but said the Congolese authorities should try to improve conditions for the second round of elections set for 22 July.
The second round will pit candidates who have not obtained an absolute majority this time against their opponents.
"What we went through is intolerable," he said. "The authorities have to do everything to improve the conditions [for elections] because Congolese citizens deserve respect."
Despite the shortcomings, some opposition political parties took part in the poll, including the Union panafricaine pour la démocratie sociale (UPADS) of former President Pascal Lissouba, who was replaced by Nguesso, and the Union pour la Démocratie et la République (UDR-Mwinda), led by former Prime Minister André Milongo.
However, the turnout was very low, a problem attributed mainly to lack of voters' cards and the late arrival of electoral materials at polling centres. According to the electoral commission, results will not be known for at least a week.
The African observers noted that security had improved and those who voted were largely not intimidated, unlike in previous elections marred by violence.