A one-off grant of £7,500 has been made available for eligible businesses.
Applications must be submitted online, even if a business has previously provided details to the council.
The UK government pledged £15m to help flood-hit firms in Northern Ireland to cover the clean-up and resume trading.
But some have criticised the amount on offer, with one trade body saying that about £37m is needed for Newry alone.
Affected business owners will also not have to pay rates until the end of March.
Stormont's Department of Finance has said that more support will be available although it is not clear how much will be on offer or when it will be available.
The Armagh, Banbridge and Craigavon council fund is limited to one payment per business.
If an individual owns several impacted businesses, each business will be considered on its own merit.
A confidential advice phone line for individuals and families who have been impacted by flooding is now in operation on 0330 135 9733.
Meanwhile, in the Newry, Mourne and Down District Council area, there have been 288 applications for Flood Emergency Business Financial Support.
More than 18 payments have been issued to date.