A passerby noticed at around 11:30 p.m. Tuesday and called Toronto Police.
The plexiglass was damaged and a statue was broken.
Gethsemane Ministries — who had put up the display — confirmed this has happened many times before.
"As millions are preparing to celebrate Christmas, a season of love, peace and joy, it is sad to see this act of hate has once again happened in Toronto," Suresh Dominic of Gethsemane Ministries said.
Dominic also said that the scene has been vandalized every year for the last seven years, with the exception of 2011.
The matter is being investigated.