Convict Naseeban Katoon says her daughter, who lives with her in Karachi central prison, was not given polio vaccination drops and caught the crippling virus, Assistant Advocate General of Sindh province Qasim Mir told AFP.
The Supreme Court has ordered an inquiry into the case and instructed all the country's provinces to disclose whether polio drops were being administered in their prisons, Mir said.
Pakistan is one of only three countries around the world where polio remains endemic, but years of attempts to stamp it out have been badly hit by opposition from militants and attacks on immunisation teams.
Katoon first raised the issue in 2009 when she applied for permission to take her daughter out of the prison for treatment, but the Supreme Court has only now heard the case.
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Shafi Mohammad Chandio, AdditionalAdvocate General (senior legal officer) for the province, said the court sought a reply from officials in Sindh within 15 days.
"The Sindh police chief has told us in writing that he has already started an investigation into whether the prison doctor had administered polio drops to the girl," he said.