The warning from the country's interim president comes as around 1,300 emergency shelters have been erected in the region's most deprived nation, enough to house up to 340,000 people.
Speaking on state radio, Jocelerme Privert said: "To those people living in houses that could collapse, it's necessary that you leave these houses to take refuge in schools and churches."
Hurricane Matthew, which has already caused major flooding in Jamaica (pictured above and below), is expected to pass close by the south west of Haiti on Monday night before moving towards Cuba.
"Some of us will die but I pray it won't be a lot," said Serge Barionette in the Haitian town of Gressier, where major storms regular cause the river to burst it's banks.
Winds of the Category four storm peaked at 145mph on Sunday evening and there are now concerns strong gusts and torrential rains could lash the areas of Jeremie and Les Cayes in Haiti.
John Cangilosi from the US National Hurricane Centre in Miami said: "Wherever that centre passes close to would see the worst winds and that's what's projected to happen for the western tip of Haiti. There is a big concern for rains there and also a big concern for storm surge."
The strongest hurricane to strike the Caribbean since Felix in 2007, Matthew could later pass through the Bahamas and to the east of Florida.
Haitians, many who are not aware of the looming storm, are being urged not to stay behind and try to protect their homes but heed evacuation warnings.
A magnitude seven earthquake which struck Haiti in 2010 left tens of thousands of people dead and the country is still rebuilding itself.
HURRICANE QUOTES
Bishop Mike Wilson from Church of God of Prophecy is from Jamaica and ministers to the West Indian community.
He told Premier's News Hour that churches need to help others.
He said: "Churches do need to open up their homes, but when you yourself are being devastated... you get pastors who lose their homes, how do you then respond to the need of the wider community when you're actually living through devastation yourself?
"That's the challenge we face."
Bishop Mike Wilson said some people, particularly those without sturdy housing, could be left with nothing.
"Unlike in the United Kingdom, people don't take out home insurance, or property insurance... because people don't trust the financial markets and that pay outs will be made, so they just take it on the chin."
He said that prayer is needed: "I think in this situation where God's people are actually in situ, we're not being saved from the devastations per say, but it's about how we reach out and touch lives.
"People need the message of the Gospel.
"They need help, they need hope."
Listen to Premier's Alex Williams speak to Bishop Mike Wilson here: