In a statement on Thursday, CBC spokesman Chuck Thompson said the edits on the eight minutes of the 120-minute film were made in 2014, before Trump was elected as President, and were not politically motivated, the BBC reported.
In the uncut version, Trump is briefly seen in a scene at New York's Plaza Hotel, when Macaulay Culkin's character Kevin asks him for directions.
Trump was the hotel's owner at the time.
The edited film was shown by CBC earlier this month, prompting criticism from Trump's supporters.
His son Donald Trump Jr tweeted a link to a story on Thursday that called the edit "pathetic".
On Thursday night, President Trump tweeted that "the movie will never be the same! (just kidding)", reports the BBC.
In a reference to Canadian Prime Minister Justin Trudeau, and well-documented disagreements between the two leaders on major policy issues, Trump added: "I guess Justin T doesn't much like my making him pay up on Nato or trade."
During a video conference call to US troops overseas on Christmas Eve, the President had described the movie as "a big Christmas hit".
Trump has made a number of cameo appearances in films, including "Zoolander" and "Ghosts Can't Do It".
( With inputs from IANS )