Stuart Hazeldine, whose production portrays the trinity as three individual people - including one woman - says scriptures were not intended to be interpreted as "black and white".
Speaking with Premier ahead of the movie's release on Friday, he said: "Scripture was written and understood to be read in allegorical ways... and yet modern society... is very much black or white, it's true or it's not but that's not the case.
"Some of our greatest writers, like C.S. Lewis, were in love with metaphor and allegory and yet many of us often struggle with that."
The picture stars Oscar-winning actress Octavia Spencer as 'Papa' or God, Aviv Alush as Jesus and Sumire Matsubara as 'Sarayu' or the Holy Spirit.
Acknowledging The Shack has caused a stir among some people, Stuart said: "I think that there were legitimate reasons for controversy and then there were some that were just a bit silly, really.
"I think the legitimate ones are discussing who is God, what is the nature of God, to what extent does Jesus's atonement cover some people or everyone - is it limited atonement, it is universal salvation.
"Those are important issues that we've been wrestling with the days of the early church fathers and that's a debate that's a great thing to have.
Based on a novel of the same name by William P. Young, The Shack tells the story of desperate father Mack Phillip who has an encounter with God after his youngster child, Missy, disappears.
Arguing that some criticism has been trivial, Stuart added: "If it's people saying 'I didn't like it because God was a black woman', I don't really have a lot of time for that because ultimately, if you read the story, you understand exactly why God chooses to present himself to the lead character, Mack, in that way."
Click here to listen to Premier's John Pantry and Rosie Wright speaking with Stuart Hazeldine: