An Egyptian criminal court sentenced ousted Islamist President Mohammed Morsi to 20 years in prison over the killing of protesters in 2012 on Tuesday, the first verdict to be issued against the country's first elected leader.

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The Cairo Criminal Court issued the verdict as Morsi and 12 other defendants in the case stood in a soundproof glass cage inside a makeshift courtroom at Egypt's national police academy.

The fall of veteran autocrat Hosni Mubarak in 2011 paved the way for what was unthinkable for decades - the Brotherhood ruling the most populous Arab country.

The man Morsi appointed army chief, General Abdel Fattah al-Sisi, toppled him in 2013 after mass protests against his rule and then launched a tough crackdown on Islamists.

Muslim Brotherhood leader and ousted Egyptian president Mohamed Morsi (Photo: EPA)

Egypt's deep state apparatus - the Interior Ministry, intelligence services and army - soon put the Brotherhood on the defensive once again.

The charge could have also led to the death penalty but an execution could turn Morsi into a martyr and embolden Islamists.

Morsi says he is determined to reverse what he calls a military coup.

While Morsi has become far less relevant, even within the Brotherhood, Sisi went on to become president, winning over many Egyptians who overlooked widespread allegations of human rights abuses for the sake of stability.

Western powers who called for democracy declined to use leverage against Sisi, the latest military man to seize power.

Sisi says the Brotherhood is part of a terrorist network that poses an existential threat to the Arab and Western world.

Morsi faces several other trials along with thousands of Muslim Brotherhood members following the military overthrowing him in 2013. He has been held at a high-security prison near the Mediterranean city of Alexandria.

The Brotherhood says it is a peaceful movement that will return to office through people power, even though demonstrations have fallen to a trickle.

Morsi in court.

Morsi, who rose through the ranks of the Brotherhood before winning the presidency in 2012, was a polarizing figure during his troubled year in office.

His policies alienated secular and liberal Egyptians, who feared that the Brotherhood was abusing power.

Protests erupted in late 2012 after Morsi issued a decree expanding presidential powers - a move his supporters say was necessary to prevent a judiciary still packed with Mubarak appointees from derailing a fragile political transition.

At least 10 people were killed in the demonstrations outside the presidential palace in December 2012, in which Morsi's supporters attacked opposition protesters, sparking clashes.

Prosecutors argued that Morsi and other Brotherhood leaders had encouraged the violence and so are responsible for the bloodshed. Morsi and his co-defendants deny the charges.

The Brotherhood survived numerous crackdowns and has been able to gain support through its charities because Egyptians longed for better services under a succession of autocrats.