Antigenic variants of H5N1 highly pathogenic avian influenza virus (HPAIV) have selected and are prevailing in poultry populations in Asia. In the present study, the potency of inactivated influenza vaccine prepared from a non-pathogenic H5N1 avian influenza virus, A/duck/Hokkaido/Vac-3/2007 (H5N1), was assessed by challenging with H5N1 HPAIV variants, A/muscovy duck/Vietnam/OIE-559/2011 (H5N1), A/whooper swan/Hokkaido/4/2011 (H5N1), and A/peregrine falcon/Hong Kong/810/2009 (H5N1) belonging to clades 1, 2.3.2.1, and 2.3.4, respectively. All chickens immunized with the Vac-3 vaccine survived without showing any clinical signs after intranasal challenge either with A/whooper swan/Hokkaido/4/2011 (H5N1) or A/muscovy duck/Vietnam/OIE-559/2011 (H5N1). After challenge with A/peregrine falcon/Hong Kong/810/2009 (H5N1), 10 out of 12 vaccinated chickens survived and the other 2 died on 4 or 7 post-challenge days. The Vac-3 vaccine of 2.4-fold antigen concentration conferred complete protective immunity in chickens against challenge with A/peregrine falcon/Hong Kong/810/2009 (H5N1).