The film, which deals with the inner dialogue of a disgruntled film critic, first bowed at the Cannes last May but the similarities were noticed only when it made its way to the Internet.
Jacqueline Cohen, Clowes' publisher, called the film "shameless theft" of 'Justin M Damiano'.
Clowes said he had never met LaBeouf and was shocked with the way his book was plagiarised, reported Buzzfeed.
"I was shocked, to say the least, when I saw that he took the script and even many of the visuals from a very personal story I did six or seven years ago and passed it off as his own work. I actually can't imagine what was going through his mind," Clowes said.
"In my excitement and naivete as an amateur filmmaker, I got lost in the creative process and neglected to follow proper accreditation. I'm embarrassed that I failed to credit Daniel Clowes for his original graphic novella Justin M Damiano, which served as my inspiration," LaBeouf wrote on his Twitter page.
"I was truly moved by his piece of work and I knew that it would make a poignant and relevant short. I apologize to all who assumed I wrote it. I deeply regret the manner in which these events have unfolded and want Daniel Clowes to know that I have a great respect for his work," the 'Transformers' star wrote.