ACL's Managing Director Lyle Shelton said the motion by Senator Richard Di Natale was rejected in the Senate today.
Mr Shelton said the opening of the each parliamentary day with the Lord's Prayer recognised Australia's cultural heritage.
"The Christian ethos underpinning western civilisation has fostered free and prosperous societies, including our liberal democracy," he said.
"It's disappointing that Senator Di Natale wanted to take away something of Australia's cultural heritage," he said.
Mr Shelton rejected comments by Senator Di Natale that faith should be a private matter.
"Everyday people bring ideas to the workplace, charities, hospitals and even parliament, formed by their values and beliefs," he said.
"The ideas emanating from the Christian faith – including those of what it means to promote human flourishing – are an important contribution in debating how best to order society," he said.
"Our democracy would be poorer if ideas emanating from any particular faith were suddenly excluded from the contest of ideas."