In the report the ministry said the boy from the Nile Delta province of Dakahlia had fallen ill with the H5N1 virus after coming into contact with infected poultry.
"He is in a good condition," Amr Kandeel, head of communicable disease control at the ministry, said in the report.
Egypt has the largest known bird flu cluster outside Asia, with 13 deaths out of the 24 reported human cases.
The government has said in the report that poultry production has recovered to 2m birds a day, the same level as before the outbreak.
The report said several weeks ago, the Egyptian government had suspected that a mutated strain of the virus with "reduced susceptibility" to the Tamiflu vaccine had emerged.
Medical experts confirmed shortly afterwards that the virus had in fact not mutated to a new and more dangerous strain transmitted between humans.