The Games organizing committee says the repairs were made months ago after an inspection found the bare concrete floors were pitted and uneven.
At the time, one committee member deemed the floors to be worse than the ones in the athletes village in Guadalajara, Mexico, which hosted the last Games in 2011.
Organizers say the floor was eventually covered with carpet in hallways and some common areas, and with dark grey floor sealing with baseboards in the athletes' rooms.
It says the carpet cost $200,000 and the sealing $1.2 million.
Organizers say the upgrade was covered by the budget for the village, which is funded by the province.
"Canada prides itself on being a welcoming and accommodating host for our international guests," TO2015 spokesman Teddy Katz said in an email.
"Unfinished floors and ragged walls without baseboards would reflect poorly on our region’s reputation as hosts. Quite simply, the village wouldn’t look finished."
The committee's CEO, Saad Rafi, said the price wasn't "exorbitant" given that there are 2,200 units in the village.