The Lancashire Festival of Hope leadership team say it's a "travesty" that Blackpool Transport chose to remove them.
The company had said it came to the decision after listening to public feedback.
A number of people had taken to social media to claim that Franklin Graham would be preaching hate and homophobia at the event which is due to take place at the city's Winter Gardens in September.
In an open letter, the church leaders said: "Because the Christian community is also a customer, we hope Blackpool Transport will listen to our public feedback as well, and not show what appears to be a potential bias against Christians."
A number of MPs have raised concern about his visit to Blackpool fearing he will repeat previous statements condemning homosexuality and Islam.
But speaking to Premier earlier this year, Graham said: "I'm not coming to preach hate, I'm here to preach about a saviour - Jesus Christ who can make a difference in our lives if we put our faith and trust in him."
The church leaders say they are seeking a meeting with Blackpool Transport and have urged Christians not to complain but to act in a positive nature by praying.
"While we pursue a fair and open dialogue with Blackpool Transport, we urge all supporters of the Festival to refrain from contacting Blackpool Transport directly, or engaging in comment via social media, about this matter," they said.
Franklin Graham has led evangelism events across the world in his role as president of the Billy Graham Evangelistic Association.
He's also reached millions of people through his aid work with the charity Samaritans Purse.
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