Thirty one premises were affected in Dungannon and four at Kinnego Marina at Lough Neagh in December.
The scheme will be a one-off.  It is not yet known how much they will get.
Agriculture Minister Michelle O'Neill had suggested some of the Â£1.3m given to Northern Ireland from a Westminster flood fund should be used to pay the compensation.
But at Thursday's meeting of the Northern Ireland Executive, it was decided to spend all that money on flood alleviation work.
Some of it will be spent on inspecting rivers and streams in areas prone to flooding.
Other money will have to be found to fund the assistance scheme for businesses.
Meanwhile, it has been announced that businesses, including farms, will also be eligible for recently announced flood protection grants.
Previously, only homeowners had been eligible for help-to-buy measures like flood barriers to protect their properties.
Businesses hit by winter flooding are to get payments under a new executive assistance scheme.