Millions of voters in the Democratic Republic of the Congo are going to the polls to cast their ballots in an election that marks the first ostensibly democratic transition of power in the vast central African country’s troubled history.

Optimists hope the DRC’s third presidential poll since the 2002 end of a civil war that killed around 5 million people will mark a turning point. Pessimists fear it will lead to a cycle of protests and repression that could lead to further chaos and renewed anarchy.

Leading opposition candidates complained of systematic harassment in the run-up to the vote, and there were fears that new voting machines could allow fraud.

Voting began at 5am (0400 GMT) on Sunday and ends at 5pm. Early signs were not good, with scores of polling stations still not open in the capital Kinshasa hours after voting should have begun, long delays at polling stations elsewhere and widespread reports of broken-down voting machines.

The election, already delayed by two years, was postponed from last Sunday to allow further time to overcome logistic challenges in a country of 80 million inhabitants spread over an area the size of western Europe with almost no metalled roads.

There will be no casting of ballots at all in three opposition strongholds after the authorities cancelled the vote there, citing health risks from an Ebola outbreak and ethnic violence. The postponement prompted violent protests last week.

Many analysts predict widespread protest by opposition supporters who will feel cheated if Emmanuel Ramazani Shadary, the hardline interior minister and the government candidate, wins.

Facebook Twitter Pinterest Emmanuel Ramazani Shadary. Photograph: Stefan Kleinowitz/EPA

The DRC’s fragmented opposition has been unable to field one unified candidate, effectively splitting the vote of those who want to see significant change in the the country.

A survey released on Friday, however, by specialists at New York University put Shadary on just 19%, trailing the frontrunner Martin Fayulu, a former business executive turned opposition candidate who was little known before the campaign, by 28 points. Félix Tshisekedi, a second opposition candidate, is on 24%.

“If elections are free and fair, an opposition candidate would be almost certain to win the presidency … The potential for violence is extremely high,” the report’s author wrote.

Almost half of the respondents to the survey said they would “most certainly and/or probably” protest against rigged elections.

The archbishop of Kinshasa, Fridolin Ambongo, held a mass on Saturday in the capital attended by Fayulu and a representative of Shadary. They and the sole female candidate, Marie-Josee Ifoku, held hands during prayer in a spirit of reconciliation.

“Unfortunately, some of our compatriots give the impression they want to hold the country hostage to violence,” the archbishop told the congregation. “In no case will we permit these elections to become another opportunity to destroy Congo and shed the blood of Congolese who have bled too much for decades already.”

One certainty is that the rule of Joseph Kabila, president since 2001, will end. Kabila’s second electoral mandate expired in 2016 and the 47-year-old only reluctantly called new elections under pressure from regional powers. He was barred from standing again by the constitution.

Kabila voted early in the morning in Kinshasa, which has endured torrential rain. “My only concern is that we have this very heavy rain and probably voter turnout might be low, but hopefully the skies will clear, and the voters will turn out in numbers,” he told reporters.

Two other major figures are absent from the ballot sheet: Jean-Pierre Bemba, a 56-year-old warlord and politician recently acquitted of war crimes by the international criminal court, and Moïse Katumbi, 53, a businessman with a big following in the south-west. Both have been barred for legal reasons.

The Catholic bishops conference said voting had not started on time at 830 polling stations, equivalent to about a fifth of the stations across the country where it had deployed observers. It also said 846 polling stations were installed in “prohibited places” such as military and police posts.

Israel Mutala, a Kinshasa-based political analyst, said voters were likely to be disappointed whatever the result. “People want to start again with new hope. They have this illusion that they can change something … but it’s an illusion. The problems are structural. An election can open the way to change but can’t go much further than that,” he said.

The DRC has refused international offers of help to conduct the elections, stating that it would compromise its sovereignty.

A limited number of observers will be present, including some from the Southern African Development Community, a regional grouping that has endorsed a number of flawed elections in recent years.

Relations with many overseas powers are tense. After prolonged EU sanctions on Shadary for his role in the brutal repression of pro-democracy demonstrators two years ago, Congo’s government ordered the bloc’s ambassador to leave the country within 48 hours on Thursday.

Officials say that “definitive” election results will be announced on 15 January, with the inauguration three days later.

The election in and around Beni and Butembo in North Kivu province, and Yumbi in Mai-Ndombe province, will be in March instead.

In Beni a few hundred protesters staged mock elections on Sunday. People cast paper ballots and sang in Swahili: “Voting is our right and nobody can stop us.”