Prime Minister Stephen Harper presented the medal to Bieber at Scotia Bank Place in Ottawa prior to Bieber's concert on Friday night.
A spokeswoman for the prime minister says the Stratford, Ont., singer's family was with him as Bieber — who was dressed in overalls for his concert — received the honour from Harper.
Erica Meekes says Harper's son Ben was attending Bieber's concert with friends.
Harper announced the presentation of the award to Bieber on his Twitter feed saying "Was happy to present @justinbieber with a Diamond Jubilee Medal today."
The medal is awarded to people who have made a significant contribution to a particular province, territory, region or community within Canada, or an achievement abroad that brings credit to Canada.
"It was a light-hearted thing," said Harper spokeswoman Julie Vaux.
"Justin Bieber is a ping pong player so they talked about ping pong and that they should meet and play ping pong next time," Vaux said.
Bieber's mother, father and grandparents also met with Harper and had their photos taken, she added.