NAIROBI — Shock waves swept through Congo on Thursday after opposition candidate Felix Tshi­sekedi was declared the winner of the nation’s presidential election, a victory seen by some as a new dawn in a country yet to experience a democratic transfer of power.

But with the announcement of the results, Congo’s electoral commission has raised more questions than answers. 

Foremost among them is how Tshisekedi came out on top, instead of Martin Fayulu, an opposition candidate whom polling had shown winning in a landslide, or Emmanuel Ramazani Shadary, the handpicked candidate favored by President Joseph Kabila, an authoritarian who has ruled Congo for 18 years. Almost no one expected this outcome, and it only deepened suspicion over a vote marred by irregularities. 

Fayulu was calm but aggrieved when he addressed the media and urged the largest election observer mission to “reveal to the Congolese people the name of the person who truly incarnated the choice of our people.”

Before he was declared the winner of Congo’s disputed presidential election, opposition politician Felix Tshisekedi spoke with The Post in October 2018. (Joyce Lee/The Washington Post)

The observer mission run by Congo’s powerful Catholic Church, the National Episcopal Conference of Congo, known as CENCO, said at a news conference Thursday that its results did not match the electoral commission’s. It had earlier told diplomats and journalists in private messages that Fayulu had won the election by the count of its 40,000 observers.

In a statement, Fayulu described the results as an “electoral holdup” that did not reflect the ballots, and he called on people to “rise as one man to protect victory.” Fayulu and other losing candidates are entitled to appeal the election results. He did not announce his intentions Thursday, but a challenge of the results in court would dash any last hopes that this could be Congo’s first uncontested democratic transition.

The dispute could ignite outrage among supporters of Fayulu’s coalition, as well as isolate Congo further from an already skeptical international community.

Most of the country remained calm, but in the city of Kikwit, about 300 miles from Kinshasa, the capital, crowds of Fayulu supporters clashed with security forces. Four people were killed, Kikwit Mayor Leonard Mutangu told the Reuters news agency.

Internet and text-messaging services remain shut down across Congo, as they have been for almost two weeks, indicating that the government may be anticipating social unrest. 

Voices of doubt were starting to trickle in from outside Congo on Thursday. 

“We must have clarity on these results, which are the opposite to what we expected,” French Foreign Minister Jean-Yves Le Drian told French media. “The Catholic Church of Congo did its tally and announced completely different results.”

Congo government spokesman Lambert Mende retorted that the French should keep out of the election.

“France has nothing to do with the vote in the Congo, and if Mr. Le Drian thinks Congo is a province or colony of France, he just needs to name the president of Congo,” Mende said.

The U.N. Security Council planned to discuss Congo’s election results Friday.

The vote was marked by widespread irregularities. In its final report, CENCO said that 38 percent of polling stations it observed were missing materials at the start of election day, and that in hundreds of cases, ballot boxes were not sealed before counting and polling stations did not properly verify voters’ identities.

A separate domestic observer mission called SYMOCEL said it witnessed 52 major irregularities, including physical tampering with results, in the 101 vote-counting centers it monitored. There were 179 such compilation centers across Congo.

The electoral commission also cited an ongoing Ebola outbreak in postponing voting in the eastern cities of Beni and Butembo, effectively barring more than a million people from the presidential vote in areas that were expected to heavily back Fayulu. The difference in the number of votes received between Tshisekedi and Fayulu countrywide was smaller than the registered voting populations in those two cities.

Tshisekedi was ultimately victorious with the support of only 17 percent of Congo’s registered voters. Turnout was just above 47 percent across the country.

In a message to The Washington Post, Fayulu accused Tshi­sekedi of entering into a “backroom arrangement” with Congo’s ruling party to steal the election from him. 

A spokesman for the ruling party congratulated Tshisekedi on Thursday. 

“Of course we are not happy, as our candidate lost, but the Congolese people have chosen and democracy has triumphed,” Kikaya bin Karubi told Reuters. The ruling party’s candidate, Shadary, was a relatively obscure choice and finished far behind Tshisekedi and Fayulu, according to the electoral commission’s results.

Tshisekedi spoke highly of Kabila in an address to supporters Thursday, calling him “an important political partner.” He also promised to rule not on his party’s behalf but for all of Congo’s 80 million people.

The overtures might have struck Tshisekedi’s father, Etienne, as a betrayal of sorts. The elder Tshisekedi spent 35 years as Congo’s most outspoken opposition figure and a constant thorn in the side of Kabila. 

Kabila so despised him that he barred Etienne Tshisekedi from being buried in Kinshasa when he died in early 2017. The younger Tshisekedi’s running mate in the election, however, was Vital Kamerhe, a former campaign manager for Kabila. 

While Fayulu loudly denounced the election’s irregularities, Tshisekedi remained mostly silent before the vote and in its aftermath.

Even if Fayulu’s allegation of a power-sharing agreement between Tshisekedi and Kabila’s party turns out to be true, the results represent a major weakening of Kabila’s position. Over his nearly two decades in power, he has consolidated authority in the office of the president, which Tshisekedi will command should he be able to weather the likely challenges to his win.