The company which has 500 hotels says it made the decision so as "not to discriminate against any religion".
Travelodge said the policy had been decided upon in 2007 and gradually implemented but customers would still be able to request a Bible at reception.
The Church of England has criticised the move.
A spokesman said: "It is both tragic and bizarre that hotels would remove the word of God for the sake of ergonomic design, economic incentive or a spurious definition of the word diversity."
Other budget hotel chains in the UK have chosen to keep Bibles in all rooms and only remove them if a guest makes a request before they arrive for their stay.
The Bible Society is calling on the hotel chain to reverse its decision.
Hazel Southam from the organisation said: "I'm really hopefully that they'll reconsider it, because you never know when you might want to open the drawer that's got the Bible in it and read it.
"You don't know when you're going to be feeling like you need something to turn to and it's great if the Bible is there on those occasions."
A spokesperson for Travelodge told Premier: "Travelodge made the decision to move copies of the Bible from its hotel rooms and place them at reception for customers to borrow in 2007.
"This decision was based on customer research and the fact that we live in a multicultural society.
"Therefore in order not to discriminate against any religion, customers who would like a Bible can pick a copy from any one of Travelodge's 500 hotel reception desks across the country, whilst staying at the hotel.
"To date, Travelodge has not received any customer feedback regarding this decision."
Hear more from The Bible Society's Hazel Southam speaking to Premier's Antony Bushfield on the News Hour: