State TV said the 67-year-old’s death was due to a cardiac arrest.
“He was buried in Medinat Nasr, in eastern Cairo, with his family present,” said Abdel Moneim Abdel Maksoud, one of his lawyers.
Morsi, also the country’s first civilian president, had appeared “animated” during a hearing in a retrial over charges of collaborating with foreign powers and militant groups, judicial and security sources told Agence France-Presse.
“The court granted him his request to speak for five minutes… He fell to the ground in the cage… and was transported immediately to the hospital. A medical report found… no pulse or breathing,” said the attorney general’s office.
“He arrived at the hospital dead at 4:50pm exactly and there were no new, visible injuries found on the body.”
Another of Morsi’s legal defence team described the moment he received news of his death.
“We heard the banging on the glass cage from the rest of the other inmates and them screaming loudly that Morsi had died,” the lawyer, Osama El Helw, told AFP.
A judicial source said Morsi had fainted during a break in the trial hearing.
The court officials “had just finished the session for the espionage case and they informed the judge that he had fainted and needed to be transported to a hospital where he later died”, he told AFP.
Morsi last saw his family in September 2018. A month later, one of his sons, Abdallah, was arrested.
Abdel Maksoud was the last member of his defence team to see the former Islamist president, in November 2017.
Morsi and nearly all leaders of the now-outlawed Muslim Brotherhood were detained after the military, then led by his successor Abdel Fattah El Sisi, removed him in July 2013 amid a wave of street protests against his divisive, one-year rule.
Internationally he received some support, but in his homeland, Morsi has a chequered legacy.
He spent just one turbulent year in office after the 2011 uprising, before being toppled by the military after millions took to the streets demanding his resignation.
The Islamist leader has been in prison since his ouster, on trial in several cases including for spying for Iran, Qatar and militant groups such as Hamas.
Morsi was also accused of plotting terrorist acts.
He was sentenced to death in May 2015 for his role in jailbreaks during the uprising that ousted his predecessor, longtime autocrat Hosni Mubarak.
Following the news of his death, Egyptian television channels labelled the Brotherhood a “terrorist group” and played a looping tagline: “The Brothers are liars”.
A group of British parliamentarians in March 2018 warned that his detention conditions had not met international standards and could lead to his “premature death”.
Other Brotherhood leaders have also died in custody.
The years following Morsi’s overthrow have seen a surge in bombings and shootings targeting security forces, particularly in the restive northern Sinai Peninsula, now a stronghold of ISIS.
Morsi’s turbulent rule was marked by deep divisions in Egyptian society, a crippling economic crisis and often-deadly opposition protests.
His death comes days before Egypt hosts the Africa Cup of Nations football tournament, starting on Friday.
Authorities have been on high alert, announcing on Facebook on Wednesday that thousands of forces would be deployed to secure venues.
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