Witnesses saw dead and sick birds inside the zoo grounds on Sunday, and the Health Ministry said that six of the 83 dead birds had tested positive for bird flu.
A ministry statement said they included species of duck, turkey and Chinese geese. The zoo has slaughtered 563 birds and drained all the ponds there, it added.
On Sunday, zoo workers sprinkled disinfectant around the cages and Talaat Sidraus, the zoo manager, told reporters the aim was to gain control of the situation "before disaster strikes".
Since the first announcement on Friday the authorities have reported cases of bird flu among poultry in at least eight provinces, stretching from Dakahlia and Biheira on the Mediterranean coast to Qena in the far south.
About 1000 poultry from private houses have been culled, along with 14,000 birds at farms north of Cairo. The authorities are in the process of slaughtering another 56,000 at a farm in the Nile Delta town of Mit Ghamr, the ministry said.
On Sunday, merchants who normally slaughter and sell live chickens on the street had closed in compliance with a ban. Some remained open but had few customers.
The government said it was importing 73,000 doses of Tamiflu, one of the few medicines thought to alleviate the symptoms of the disease when it hits humans.
No human cases have been diagnosed so far in Egypt.