Chibly Langlois says the practice offers 'magic' to the poor population but no proper solutions.
The cardinal says the conditions people live in is forcing them to look for supernatural help instead of coming to the Catholic Church.
About 80% of all Haitians are Catholic although a report says 50% practice voodoo but normally in private.
Cardinal Langlois said: "It's a big problem for the church. And for Haiti".
"The church cannot – and does not – ignore the cultural elements and uses of voodoo, like the drum, the rhythm, the way of singing.
But you can't be voodooist and Catholic. The Catholic should be pure Catholic; the voodooist should be pure voodoo," he said.
Voodoo was banned in Haiti until 2003 when it was given legal recognition as a religion with equal standing to Catholicism.