Khaled Al-Qazzaz's family earlier said the father of four had received all of the needed documents to leave Egypt and expected to arrive in Toronto on Thursday.
But late Wednesday, Al-Qazzaz's brother-in-law said Al-Qazzaz, his wife Sarah and their four children were stopped at Cairo's airport and told they could not leave.
The statement from Ahmad Attia also said their passports were taken and savings intended for Al-Qazzaz's medical costs were confiscated.
The family has said returning to Canada would mean the 35-year-old would soon be able to have much-needed surgery in Ontario for a severe spinal condition, said to be related to his detention.
"There has been no explanation by Airport Security Services as to why the family is currently being held," said Attia.
"Sarah and the children are extremely exhausted and distressed by the current circumstances."
Al-Qazzaz, a University of Toronto engineering graduate, was once an aide to Egypt's ousted president Mohammed Morsi and was arrested alongside the former leader in July 2013, when the Egyptian military removed Morsi from office.
Al-Qazzaz was never charged, nor did Egyptian authorities explain why they had arrested him.
Towards the end of last year, due to his deteriorating health, Al-Qazzaz was transferred from solitary confinement to a hospital in Cairo, but remained under detention. He was released from custody in January.
His case had attracted attention from human rights activists and groups such as Amnesty International.
Former foreign affairs minister John Baird had also raised the case with the Egyptian government.