Safwat Khalil, 59, died in prison on Thursday, shortly after a court ruling ordering his release.
He was arrested last month along with scores of Brotherhood supporters on charges of inciting violence and possession of weapons.
A member of his defense team said Khalil's health had deteriorated after being transported to court by a police truck instead of an ambulance.
His death sounded the alarm about many Muslim Brotherhood detainees who need constant medical attention.
A senior member in the group's legal committee, who asked not to be named, told Anadolu Agency that scores of Brotherhood members have health problems but have been denied release on health grounds.
Egyptian authorities unleashed a massive crackdown on Muslim Brotherhood leaders and sympathizers following the military's overthrow of elected President Mohamed Morsi, a Brotherhood leader himself.
Hundreds of the group's senior and mid-ranking members are currently detained over various charges, including incitement to murder and violence and involvement in attacks on state and private properties.
The Brotherhood source said that over 12 members suffer chronic illness in Cairo and Giza alone.
Among them was former supreme guide Mahdi Akef, 86.
He was the only member allowed to be moved to hospital for treatment.
However, several others were not able to get similar medical treatment, including ailing current supreme guide Mohamed Badie and his deputy Khairat al-Shater, who suffers diabetes and pressure.
A pro-Morsi legal group, the Front of Judiciary Independence Against Coup, also voiced its worry over the health conditions of Brotherhood detainees, saying they are mistreated and held at "illegal" locations.
A security official, who asked not to be named, dismissed the claims, saying that prison authorities always provide the best medical treatment possible to all prisoners in accordance with international standards.
"All prisoners undergo several medical checks once they are moved to prison, and those with health problems receive special treatment, regular checks and all needed medicine," the source told AA.
"All Brotherhood members were subject to the same treatment and they were allowed to receive medication from outside," he added.