Mr. Habineza, a former journalist, said in an interview on Saturday that the results were “indeed not pleasing as we had expected.”
The portents of defeat seemed clear at one of Mr. Habineza’s last campaign rallies. Held on a roadside in the outskirts of Kigali, the capital, only 500 people showed up. Chickens darted around while half the crowd stood across the street, listening from a distance.
By contrast, at the president’s final campaign rally on Wednesday on a hilltop near Kigali, more than 200,000 people sang, danced and cheered while waving the party flag.
“Kagame really changed the lives of the people, so we have to vote for him,” said Chaste Uwihoreye, 39, a clinical psychologist who lost both parents in the 1994 genocide that left 800,000 Tutsis dead.
He credited Mr. Kagame, who led rebel forces to stop the massacre, with uniting and reconciling Rwandans while expanding the country’s economy.
Mr. Habineza acknowledged that some people in Rwanda fear criticizing the government. In 2010, his party’s vice president was found beheaded weeks before the elections. Other opposition parties have faced violence and harassment.
Still, he said, “No one will ever intimidate me.”
More than 6.6 million Rwandans cast ballots for Mr. Kagame, according to the official tally. Just over 80,000 voted for the opposition. The government said turnout totaled 96 percent.
Mr. Kagame’s victory has raised concerns that Africa’s “forever presidents” club will gain a new member and embolden other leaders in the region who wish to cling to power. Such comparisons have been rejected by Mr. Kagame’s backers.
The postelection mood was somber for the new People Salvation Movement, which says that it has been systemically persecuted by Mr. Kagame’s loyalists. Fifteen of its members met inside a gated house, curtains drawn and doors shut, to discuss future strategy.
Diane Rwigara, 35, an accountant who leads the group and was once considered a strong contender against Mr. Kagame, said she was fighting against fear. “People get mistreated by the government, by people of power, and they choose to keep quiet,” she said.
Ms. Rwigara said she had submitted almost double the required signatures to qualify as a presidential candidate, but was rejected by the electoral commission in July. She said the influence of Mr. Kagame’s party over the commission meant it had “no capacity to organize free and fair elections.”
The consequences of her intention to challenge Mr. Kagame came quickly.
Fake nude photos of Ms. Rwigara circulated on the internet. The Rwandan tax agency demanded $6.6 million from her family’s tobacco business for taxes, penalties, fees and interest. Her family’s bank accounts have been frozen and businesses shuttered, surrounded by state security forces.
“It’s because I spoke out,” she said. “They don’t just kill you physically you. They kill you financially, too.”
Plainclothes government security forces seized the co-founder of her movement on Dec. 26 after he had given an interview in a local newspaper, Ms. Rwigara said, and “nobody knows” where he is.
At a rural polling station about an hour outside Kigali, Charles Ndamage, who voted for Mr. Habineza, said his neighbors had threatened him for supporting an opposition candidate.
“In the village, you can be treated as an enemy of the country,” Mr. Ndamage said.
Ida Sawyer, the central Africa director at Human Rights Watch, said that under Mr. Kagame, independent news media have been silenced and rights organizations are almost nonexistent “after years of intimidation and interference.”
Boniface Twagirimana, the vice president of the United Democratic Forces of Rwanda, said his party had been forced to operate illegally after the government rejected its repeated registration applications.
Mr. Twagirimana claims plainclothes intelligence operatives tried to kidnap and strangle him in Kigali more than two years ago.
“We can even die. Every day we wait for those people who finish us anytime,” he said.
In March 2016, a member of Mr. Twagirimana’s party disappeared, according to Amnesty International, and last May, a party representative’s body was found mutilated. The party’s chairman is serving a 15-year prison sentence on charges of terrorism and threatening national security, after running for president in 2010.
The outcome of political repression in Rwanda, Mr. Twagirimana said, is that Mr. Kagame “is competing against himself.”
Mr. Gasamagera, the spokesman for Mr. Kagame’s party, rejected such criticism as unwarranted. He said Rwanda had a “free and open environment for freedom of expression.”
Nine of the 11 registered political parties in Rwanda endorsed Mr. Kagame in his presidential run. A 2015 constitutional referendum approved by 98 percent of voters allows Mr. Kagame to potentially remain in power until 2034.
At Rwanda’s electoral commission headquarters in downtown Kigali, the commission’s executive secretary, Charles Munyaneza, said he had been “very satisfied” with the voting process.
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