In November, a highly anticipated report on the voting process from Brazil’s military said it found no evidence of any irregularities. It also said that the nature of Brazil’s fully digital voting system meant it could not decisively rule out a specific fraud scenario.

Independent security experts generally applauded the report, saying it was technically sound. They had pointed out the same hypothetical fraud scenario in the past — government insiders inserting sophisticated malicious software onto Brazil’s voting machines — while also stressing that it was extremely unlikely.

Brazil finds itself in a tricky situation. Security experts say its electronic voting system is reliable, efficient and, like any digital system, not 100 percent secure. Now politically motivated actors are using that kernel of truth as reason to question the results of a vote in which there is no evidence of fraud.

For years, Mr. Bolsonaro has attacked Brazil’s election system as rife with fraud, despite a lack of evidence. As a result, three out of four of Mr. Bolsonaro’s supporters now say they trust Brazil’s voting machines only a little or not at all, according to polls.

To ease those concerns, election officials invited Brazil’s military to a transparency committee last year. It was seen as a gesture to Mr. Bolsonaro, a former Army captain who had stacked his administration with generals. Quickly the military began echoing some of Mr. Bolsonaro’s criticism, raising worries in a nation that had suffered under a military dictatorship until 1985.

Eventually, the military and election officials agreed to some changes to voting-machine tests.

Mr. Bolsonaro’s supporters have pushed videos of malfunctioning voting machines, unattributed reports of foul play from election officials and inaccurate analyses of voting returns as proof of something amiss. Independent experts have examined the claims and said they have no validity.

Three hours after the polls closed, computers had counted virtually all 118 million votes. That efficiency is in part because Brazil is the only country in the world to use a fully digital voting system, without paper backups. Yet for years Mr. Bolsonaro has framed that lack of paper backups as a vulnerability that throws any election into question.

The military said that its technical experts found no inconsistencies in the voting process or in the results of the two national votes last month. It also said that election officials had not allowed its experts to fully inspect the voting machines’ 17 million lines of computer code and that officials did not test enough machines on Election Day to rule out the possibility that they contained malicious software that could manipulate vote counts.

“It’s very technically correct,” said Marcos Simplício, a cybersecurity researcher at the University of São Paulo who tests Brazil’s voting machines.

Still, Mr. Simplício and other experts have said that the machines are highly safe, with layers of security designed to prevent fraud and errors. Mr. Simplício’s team of cybersecurity researchers, for instance, have tried to hack the machines to no avail. That is in part because the machines are not connected to the internet, making them virtually impossible to manipulate without physical access, and because they are encrypted and use technology to protect their encryption keys similar to that used in iPhones.

Yet, experts have pointed out one scenario that appears possible. A group of government engineers who write the machines’ software could insert malicious code to change votes. But to do so, multiple engineers would need to act at the exact right time and work together without detection. And the malicious code would have to be sophisticated enough to recognize a test of the machines and deactivate itself for the duration of the test.

Security experts generally back the concept of paper backups, which has been pushed by Mr. Bolsonaro. But they also warn it would introduce another variable that could be attacked by bad actors — or, perhaps more important, exploited by those claiming voter fraud.

Mr. Bolsonaro, who authorized his government to transition to his opponent in the election, Luiz Inácio Lula da Silva, on Sunday criticized the actions of his supporters, saying on Twitter that peaceful demonstrations are part of democracy, but that “destruction and invasions of public buildings, like what occurred today,” are not.