Around 20 websites based in Qatar and Egypt have been inaccessible since Wednesday night, including the Doha newspapers Al-Watan and Al-Raya, the Muslim Brotherhood's Ikhwan Online and Egypt-based Al-Sharq television which is close to the outlawed group.
Independent sites such as Mada Masr, which takes a strong stand against corruption, and Huffpost Arabi, the Arabic edition of the Huffington Post, have also been cut for Egyptian web surfers.
It is not the first time that Al-Jazeera has run foul of Sisi's administration.
Cairo has accused the network of supporting the Muslim Brotherhood which it blames for violence after Sisi ousted the movement from power in 2013.
Three Al-Jazeera journalists, including a Canadian and an Australian, were detained between 2013 and 2015, triggering international protests.
Timothy Kaldas, a non-resident fellow at the Washington-based Tahrir Institute for Middle East Policy, said the latest crackdown appeared to be aimed at curbing discontent in Egypt and enacted without fear of consequences.
"More and more people are frustrated in Egypt in general. So they want to stop the critical information which could increase the frustration," he said.
And after Sisi met US President Donald Trump last weekend, Cairo had "realised there will be no pressure coming from the United States ... whereas before they would have been criticised".
- Down tools and stay silent -
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On Thursday, Mada Masr posted on its Twitter account a cartoon of a man in front of a closed wooden door standing in the desert with the caption: "We have confirmed Mada Masr's website has been blocked. Stay tuned on how to find us again."
Huffpost Arabi, in a tweet of its own, calls on readers to use its Facebook page.
An anti-terrorism law, adopted in August 2015, lays down stiff penalties for publishing "false information" on attacks in Egypt that contradicts official reports from the country's defence ministry, stirring condemnation from rights groups.
A growing list of media personalities have since either decided to down tools and stay silent or run into trouble with the judiciary.
In March, a former head of Egypt's journalists' union, Yehya Kallache, and two aides were handed suspended one-year prison sentences for having sheltered two journalists on the run.
Heart surgeon-turned-comedian Bassem Youssef used to host the most popular political satire television show in the history of Egypt, the Arab world's most populous nation.
Dubbed Egypt's Jon Stewart, Youssef ignored all the rules governing the state-controlled media, lampooning politicians from across the spectrum.
But his show "El Bernameg" went off the air in 2014 and he left the country with his family to resettle in Los Angeles.
Such cases have added fuel to accusations by rights activists that Sisi is running an ultra-authoritarian regime which has suppressed all opposition since the military toppled Islamist president Mohamed Morsi.
In the 2017 press freedom index published by watchdog Reporters Without Borders (RSF), Egypt ranks 161st out of 180 countries.