But he says Tony Abbott's "strong Christian faith" could benefit him.
The provocative comments triggered heated debate on Perth talkback radio yesterday as a string of callers objected to the apparent leap into partisan politics.
The archbishop told The Australian he had not meant to imply people should not vote for the Prime Minister - a self-professed atheist - and was simply "sounding a caution" about the rise of secularism in politics.
"I had no intention of attacking Julia Gillard at all. My point was the future, not the present - that if the people who don't subscribe to any religion get stronger, we might have a repeat of what happened in Europe, where the church was sidelined," he said.
Ms Gillard declined to respond directly but said she respected the work done by the Catholic Church and other religious groups.
The archbishop's comments follow attacks by two other church leaders in recent months - Sydney Anglican Archbishop Peter Jensen and Sydney's Catholic Archbishop Cardinal George Pell - who warned against atheism.
The Perth archbishop sparked yesterday's debate with a statement he sent to The West Australian newspaper on July 22, which was not published until yesterday.
Titled "Comments on the forthcoming election", it said many Christians were concerned "someone who does not believe in God may not endorse the Christian traditions of respect for human life, for the sanctity of marriage and the independence of churches.
"Some will undoubtedly vote for Mr Abbott because they appreciate his strong Christian faith (but) this might be counter-balanced by others who see it as a negative," he said.
SIC: TAAUS