Morsi was buried early in the morning alongside other senior figures of the Muslim Brotherhood, his son, Ahmed Morsi, said on his Facebook page.
The burial was attended by members of the family in Cairo's Madinat Nasr after authorities refused to grant permission for a burial in Morsi's home province of Sharqiya in the Nile Delta, Ahmed Morsi said.
"We washed his noble body at Tora prison hospital, performed prayers for him in the prison mosque … the burial was at the cemetary for Muslim Brotherhood spiritual guides," Ahmed wrote.
Morsi's lawyer, Abdel Moneim Abdel Maksoud, confirmed the burial took place in the public cemetery early on Tuesday.
Al-Wafaa Wa al-Amal cemetery in Cairo where Morsi was buried [Khaled Elfiqi/EPA]
Morsi, who was a leading figure in the Brotherhood, became Egypt's first democratically elected president in 2012, one year after the Arab Spring uprising saw the end of President Hosni Mubarak's 30-year rule.
He was deposed in July 2013 following mass protests and a military coup led by Egypt's current President Abdel Fattah el-Sisi, after which he was immediately arrested. He had been in detention ever since.
The Brotherhood, which has since been outlawed, said Morsi's death was a "full-fledged murder" and called on Egyptians to gather for a mass funeral.
Security officials stood guard outside the cemetery were Morsi was buried [Khaled Elfiqi/EPA] [Khaled Elfiqi/EPA]
In a statement on its website, the Brotherhood also called for crowds to gather outside Egyptian embassies around the world.
Meanwhile, observers on social media decried the apparent haste with which Morsi's burial was carried out.
"The sudden, abrupt and restricted manner in which the Egyptian regime has enforced President #Morsi's burial, raises even more questions regarding the circumstances of his death, and intensifies calls for an independent medical enquiry," Anas Altikriti, founder of The Cordoba Foundation, said on Twitter.
Mahmoud Refaat, a foreign policy advisor at the European Institute for International Law and International Relations said the burial went against Egyptian tradition.
"In Egyptian tradition, which is considered quite sacred, we bury our dead during daylight hours, either after the duhr (noon) or afternoon (asr) prayers," Refaat said on Twitter.
"It is also done where the dead was born. Forcing Morsi's family to bury him in the middle of the night with only two of his sons present, and without his wife, only confirms that Egypt (authorities) has no honour and is being ruled by the Emirates," he added, refering to the political ties between the government of el-Sisi and the United Arab Emirates.
Al Jazeera has not been able to verify who was present at the burial.
The news of Morsi's death quickly spread through Egypt's prison population, sources within two prisons told Al Jazeera.
A source at a facility in the Nile Delta, who asked not to be identified, described emotional scenes as prisoners learned about the ex-president's demise.
Speeches were given by senior prisoners, the source said, adding that some inmates were "crying as if they cried for a dear family member".
"We cried for the symbol that was lost, and we cried of the deterioration of the prison conditions," the prisoner said.
Grief quickly turned into anger among some of the younger inmates, the source said, adding that senior prisoners stepped in to calm the situation.
'Mistreatment of detainees'
There have been reports over the years that Morsi had been mistreated and tortured in jail, with activists saying on Monday his death should be seen in the context of the Egyptian authorities' systematic isolation and mistreatment of political detainees.
Human Rights Watch called the news of Morsi's death "terrible" but "entirely predictable", citing the government's "failure to allow him adequate medical care".
"The government of Egypt today bears responsibility for his death, given their failure to provide him with adequate medical care or basic prisoner rights," the group said in a statement to Al Jazeera.
In 2015 an Egyptian court sentenced Morsi to 20 years in prison over the killing of protesters during a 2012 demonstration outside the presidential palace in Cairo [Ahmed Ramadan/Anadolu Agency/Getty Images]
Amnesty International said the Egyptian government bears responsibility for the death of the former president, amid pressing international demands for a fair and transparent investigation into the circumstances surrounding his final hours.
Rami Khouri, from the American University of Beirut, said military governments in the Middle East and North Africa are now worse than ever in the treatment of their civilian populations.
"The extent of the brutality of which the Egyptian and other Arab governments are doing – jailing tens of thousands of people, arresting people simply because of an opinion they expressed on social media, preventing any kind of free media … as well as torture and fake trials – this is much worse than it's ever been in the Arab world," Khouri told Al Jazeera.
"This is the double tragedy. Not only were Morsi and the Muslim Brothers and their democratic allies crushed after 2012, but the pressure against them has become even more brutal … These things need to be exposed to daylight and be analysed honestly and accurately."
According to Egyptian authorities, a medical report showed no apparent recent injuries on Morsi's body.
The 67-year-old, who had been behind bars for nearly six years, had a long history of health issues, including suffering from diabetes, as well as liver and kidney disease.
Morsi, who was facing at least six trials, was serving a 20-year prison sentence for a conviction arising from the killing of protesters during demonstrations in 2012. He was also serving a life sentence for espionage in a case related to the Gulf state of Qatar.
Other charges against the former president included jailbreak, insulting the judiciary and involvement in "terrorism".
His supporters say the charges against him were politically motivated.
In November 2016, the Court of Cassation scrapped the life imprisonment sentence for Morsi and 21 other defendants, including some who had received the death penalty in the same case, and ordered a retrial.
Throughout his imprisonment, Morsi was only allowed three visits from his family.
Turkish President Recep Tayyip Erdogan was the first world leader to pay tribute to Morsi, calling him a "martyr."
"May Allah rest our brother Morsi, our martyr's soul in peace," said Erdogan, who had forged close ties with the late former president.
Erdogan blamed Egypt's "tyrants" for Morsi's death.
"History will never forget those tyrants who led to his death by putting him in jail and threatening him with execution," Erdogan said in a televised speech in Istanbul.
Egypt's Morsi: The Final Hours
SOURCE: Al Jazeera and news agencies