Department of Conservation staff on a routine visit to the reserve at Karapiro, 32km south-east of Hamilton, discovered the dead birds yesterday.
Two remaining kiwi in the reserve were rescued and transferred to a safe haven at Rainbow Springs, Rotorua.
Waikato Conservator Greg Martin said the fenced reserve has been free of threats to kiwi for several years and had provided a nursery for kiwi chicks, allowing them to reach a kilogram in weight, at which size they were generally able to fend for themselves in the wild.
"About 65 kiwi chicks have been successfully raised in the specially fenced reserve since 2002 and transferred back to their home forests. Smaller birds are most vulnerable to attack and at least three of the dead chicks displayed bite marks consistent with an attack by a wild cat or possibly a large ferret," Mr Martin said.
The dead birds would be taken to Massey University for a post mortem to determine the exact cause of death.
"The department will be undertaking a full and urgent investigation to answer all the how, why and when questions. It is a tragic loss of 11 precious kiwi chicks and devastating news for the department staff directly involved in the kiwi recovery programme."
All the dead kiwi were brought to the reserve from Tongariro Forest.
Tuwharetoa iwi spokesman Bubs Smith said the cultural impact of losing such a large number of taonga (treasures) was "devastating" and the setback would be felt in Tongariro Forest for a number of years to come.
