The birds, named Stumpy and Casper, were huddled around their water bowl the day before their deaths.
The birds, thought to be over 40 years old, had been gifted to his late wife Dawn in 1977 who was a well-known parrot breeder.
DOC Mahaanui district operations manager Andy Thompson said the news was shocking and the death of the birds was "unintended and deeply concerning".
"We offer our sympathy to Ron Stewart and his family," Thompson told Stuff.
DoC's website estimates the bird's population as between 3000 and 7000, with the Southern Alps the only place in the world where the alpine parrot can be found in the wild.
Kea are protected by law, with the Wildlife Act declaring a maximum fine of $100,000 or six months in prison for anyone convicted of killing one.