Hamza, 49, dubbed the "preacher of hate", is serving seven years for inciting the murder of non-Muslims.
In a letter to a London-based Islamic organisation, Nagat Mostafa, 46, said her husband claimed to be the victim of racist bullying and Islamophobia in Belmarsh jail.
Her letter to al-Maqreze Centre for Historical Studies was sent shortly after Hamza - who is fitted with hooks on both hands - underwent surgery in May to remove an inch of bone from his left arm stump, which had become infected.
She wrote: "I would like to bring to your attention the current plight of my husband…
"The reason that his arm needed further amputation was because of the removal of his prostheses, resulting in him constantly putting pressure on the remainder of his fore limbs. As there is no soft furnishing in his cell, he has been suffering considerable pain… After surgery, before he had even recovered from the anaesthetic, he was returned to Belmarsh, only to be told he had to move from his cell to another one. He was so weak and unable to stand that he refused, resulting in him being put in solitary confinement…
"My husband says the racist bullying and Islamophobia against him have intensified."
The contents of the letter were disclosed by the Maqreze Centre, which called the cleric's treatment "unjust" and said it feared he could die behind bars.
He could die behind bars? Oh, the humanity! I shed a bitter tear.