Muecke was honoured by Australian Prime Minister Scott Morrison at an Australia Day ceremony in Canberra on Saturday night.
A South Australian who began his medical career in Kenya, Muecke in 2008 co-founded Sight For All, an organization that aims to deliver eye health care free of charge around the world.
Accepting the award he described type 2 diabetes, the leading cause of blindness in adults, as a "looming catastrophe for our health system."
"It's a growing epidemic and it's the biggest threat to our health system," he said.
"In 2020, I'm going to continue my fight for the right to sight."
However, he said that he would have 12 months to draw attention to the disease, instead using his speech to focus on Australia's bushfire crisis.
"The uncompromising bushfires that have swept through our country have left widespread disruption and heartbreak in their wake, and few of us remain untouched," Muecke said.
"Too many people have lost their lives, and the devastation of our landscape and iconic wildlife is beyond belief.
"And all of this on the back of the unprecedented droughts and floods that have tortured our beloved country and farming communities over the past few years - my thoughts are with all who've been affected."
Tennis player Ash Barty, who finished 2019 ranked number one in the world, was named the Young Australian of the Year for inspiring fans while obstetrician John Newnham received the Senior Australian of the Year.