Cognition Education Trust sponsor the award and executive director, Anne Rodda, said Mr Griffin was an "outstanding educator".
"It is a privilege to celebrate Brent's leadership of an energetic school community that is collectively committed to enhancing every student's potential."
Leadership recipients go through a "rigorous" selection process to reach the national awards.
They are first nominated by a parent, board member, trustee, parent or community organisation, which is then followed by the teacher submitting a comprehensive self-portrait and teaching background.
Regional recipients are selected who then give a five minute presentation to the judging panel and submit a paper on a topic of their interest to be considered for a National Excellence in Teaching Award or a National Excellence in Leadership Award.
When the award was announced, the whole school did a haka in Mr Griffin's honour.
Mr Griffin said he was "incredibly proud" of being principal at Western Heights Primary and receiving the award was "overwhelming".
"I was having an out-of-body experience because I heard all these wonderful things being said about this person, only to realise they were talking about me. It's all very overwhelming and I couldn't have done it without my amazing staff."
Mr Griffin said he loved his job and planned to continue doing it for many more years to come.
"We are working as hard as we can to support our amazing community and this award is about us, not me. I couldn't have asked for a more dedicated team and I am truly grateful."
Mr Griffin said he would put the $5000 prize money towards a global study tour, visiting the Hackney Learning Trust in England, the A. B. Combs Magnet Elementary School in Raleigh, America and Rosyth School in Singapore.
