One of the outbreaks killed 5,431 birds out of an 11,000-strong flock on a farm in Boankra in the Ashanti region, while the other killed 5,935 out of 13,188 birds on a farm in Nkawkaw in the Eastern region, the report said.
The remaining birds in the flocks were all slaughtered.
The outbreak in Eastern region followed the illegal movement of birds from the outbreak farm in Ashanti, the report added.
Ghana earlier this year reported an outbreak of highly pathogenic H9N2 bird flu on a farm in the southwest.