Abu Hamza was scheduled to enter pleas on 16 charges from Belmarsh Prison but refused to leave his jail cell, The Times of London reported.
Instead, a prison officer appeared and said the 47-year-old was being examined by medical staff at the high security prison.
"He is complaining his toenails are too long," prosecutor Adina Ezekiel said, before asking the judge to order Hamza produced in person at the Old Bailey for future appearances.
Judge Peter Beaumont remanded Hamza back into custody for 14 days and ordered set a tentative trial date of July 4.
Hamza, who has no hands and only one eye, is accused of soliciting others at public meetings to kill non-believers, including Jews.
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