Human Rights Watch said the three-day vote on a set of constitutional amendments, which concluded Monday, was "marred by serious flaws," including reports of citizens being forced to vote or bribed with food and money.
"The constitutional amendments are a shameless attempt to entrench the military's power over civilian rule, and the referendum took place in such an unfree and unfair environment that its results can have no pretense to legitimacy," Michael Page, the group's deputy director for the Middle East and North Africa, said in a statement issued after the results were announced Tuesday.
El-Sissi's "desire to demolish an independent judiciary and secure his autocratic rule for at least 11 more years is re-creating the impoverished and repressive political environment that drove Egyptians to revolt against former President (Hosni) Mubarak in 2011."
Authorities said Tuesday the amendments were approved by 88.83% of voters, with turnout of 44.33%. The constitutional amendments extend the presidential term from four years to six years, but include a special clause extending el-Sissi's current term to 2024 and allowing him to run for another six-year term.
The amendments recognize the military as the "guardian and protector" of the Egyptian state and give military courts wider jurisdiction for trying civilians. They will also allow el-Sissi to appoint top civilian judges.
El-Sissi led the military overthrow of an elected but divisive Islamist president in 2013 and was elected president the following year. Last year he was re-elected after all potentially serious challengers were arrested or pressured to withdraw from the race.
Authorities have waged an unprecedented crackdown on dissent since 2013, rolling back freedoms gained in the original uprising. Thousands of people have been jailed, including a number of prominent pro-democracy activists. Local media is dominated by pro-government figures, and vaguely written laws prescribe jail time for any perceived criticism of the government or military.
Ahmed Badawi was arrested in Cairo on Saturday while holding a sign that read "No to the constitutional amendments," according to Doaa Mustafa, a human rights lawyer. The Egyptian Commission for Rights and Freedoms said a local police station confirmed his arrest. The NGO said he has been questioned by the national security agency.
During the three-day referendum, voters were offered free rides or food parcels in exchange for voting, in efforts organized by pro-government businessmen, The Associated Press reported. The Arab League said Wednesday that its monitors witnessed similar activities.
At least five people in and around Cairo said they saw police stop microbuses and check that all passengers had red ink on their fingers from voting. Those who did not have ink on their fingers were ordered off the buses and told to vote.
"They took our IDs first, then they checked our fingers," said Ahmed Kassem, a 28-year-old worker in a dairy shop. "I had already voted and had my finger inked. When the officer saw the ink, he let me go." Two other people confirmed the incident, speaking on condition of anonymity for fear of reprisal.
Two other individuals said police stopped their microbus at a temporary checkpoint near Cairo University. They said police took them and five other passengers to a local police station, where they were held for more than an hour until the polls opened. Then they were taken to a nearby polling center and told to vote.
The two individuals, who also spoke on condition of anonymity for fear of reprisal, said they were not told whether to vote yes or no. Police spokesmen did not respond to multiple calls requesting comment.
In a departure from previous votes, authorities allowed people to cast ballots outside their home provinces. A judge overseeing a polling center in Cairo's Manial neighborhood said it "made the difference" and was key to boosting turnout. The judge spoke on condition of anonymity because she was not authorized to brief reporters.