"On Monday December 29, 2014 the attorney general issued an order for Khaled al-Qazzaz's release. Today, Khaled was released from his hospital room," the family said in a statement.
Qazzaz, an advisor to Morsi on foreign affairs, was arrested along with hundreds of other aides and members of his Muslim Brotherhood on July 3, 2013, the same day the army deposed the former president.
"He has a problem with his spinal cord," his brother-in-law Ahmad Attia said from Toronto where the family is based.
"He has shifted his disk. There is a risk of permanent paralysis," he said in the English-language statement.
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In November, Qazzaz was transferred from prison to a private hospital and has since undergone surgery, the family said.
His relatives hope to take him soon to Canada for further treatment.
Qazzaz is a permanent resident of Canada, while his wife and four children hold Canadian nationality.
Since Morsi's overthrow, a government crackdown on his supporters has left more than 1,400 people dead, most of them in August 2013 when police broke up two pro-Morsi protest camps in Cairo.
Thousands of Morsi supporters have been imprisoned, and dozens sentenced to death after speedy trials.
Morsi is also behind bars and facing trial on a number of charges.