The 18-year-old singer collected the award on Friday in Ottawa, Canada ahead of his concert at Scotiabank Place, reported Aceshowbiz.
PM Harper took to Twitter to address the encounter. "Was happy to present @justinbieber with a Diamond Jubilee Medal today," he wrote and posted a picture of him shaking hands with the teen pop idol.
Bieber is one of 60,000 Canadians who receive the medal which was created to mark the 60th anniversary of Queen Elizabeth II's accession to the throne this year. It's presented to honor "significant contributions and achievements by Canadians."
Some twitter users criticized the singer's choice of outfit, which consisted of overalls on top of a white T-shirt, completed with a baseball cap.
One Twitter user wrote, "I cannot believe what Justin Bieber wore to accept the diamond jubilee award from Stephen Harper today. Embarrassing," while another said the way he dressed made him look "like a farmer or someone who's ready to paint walls."