The account of the conservative Catholic think tank was closed today "due to repeated or severe violations of our terms of service".
When Google spokeswoman was asked what the "repeated violations" were she would not comment “on an individual account” referring instead to YouTube's community guidelines.
David Quinn, director of the Iona Institute said he had "no idea" why the account had been closed and was attempting to get an answer from Google.
"I just got an email about it this morning, with no explanation or any number to contact. The only video of ours that I can think of is about marriage and the case for man/woman marriage. I can only imagine it’s that and objectively speaking there is nothing offensive in it."
The video, which is still available on the Vimeo site, is an animated series of images and text, voiced over by a young man and young woman, arguing heterosexual and homosexual partnerships are essentially different as "only a man and a woman can make new life".
"Only a man and a woman can give a child a mum and a dad. No two men and no two women can ever do this. So it makes sense to treat something unique in a unique way. That’s not discrimination," it says.
Mr Quinn said all other videos the Institute had posted were of people giving talks.
He said the Case for Man/Woman Marriage video had been on the YouTube site since before Christmas.
According to YouTube's community guidelines: "We encourage free speech and defend everyone's right to express unpopular points of view. But we don't permit hate speech (speech which attacks or demeans a group based on race or ethnic origin, religion, disability, gender, age, veteran status, and sexual orientation/gender identity)."
Mr Quinn said there was "nothing in this video that resembles hate speech".
"I think this is a very worrying development. Does it mean YouTube has a new policy where any view in favour of traditional marriage is banned? Or is it that someone in Google in Ireland didn’t like the video? Because if either of these is the case it amounts to censorship."
He said there were numerous other examples of videos in favour of man-woman marriage on YouTube, including ones by the US-based National Organisation for Marriage.
"It is extremely unfair that we have been singled out like this," said Mr Quinn.