Pete left a message on his Facebook page for his dad, who was one of his biggest supporters.
Don Bethune asked the Government to take a tougher stance on his son's behalf when Peter was charged with trespassing after he boarded the Japanese whaling boat the Shonan Maru 2 in 2010.
"RIP Dad. I've been on patrol with some people in a remote coastline and just got the news that Dad passed away 3 days ago," Bethune wrote.
"He was an amazing man in many ways. Super generous and always saw the best in people. We will all miss him dreadfully."
Mary Russell-Bethune said her family were at peace with Don's death.
It had been a tough year for the Bethune family. In January Pete's twin brother Barry Bethune saw his son Shaun Bethune, 23, and best friend Lindsay Cullen, 59, die of hypothermia in the icy waters of the Foveaux Strait after their boat capsized.
Don Bethune's funeral will be held on Tuesday at 1.30pm in the Avalon Chapel in Hamilton.