The H5N1 virus was detected in the boy from the northern province of Al Gharbiyah after he came into contact with poultry, the spokesman said.
The boy is currently in a stable condition and is receiving treatment.
Earlier this week, a 4-year-old Egyptian boy from the province of Sharqiya in the country's northeast was hospitalized with bird flu.
Egypt's first case of bird flu was recorded in 2006, since when at least 26 people have died after contracting the virus.
Although there have been no incidences of human-to-human infection, experts fear that the bird flu virus may mutate into a form that could be easily transmitted from person to person, causing a global pandemic.