Some 12,000 sandbags have been deployed as areas in the east of Northern Ireland have been hit with flooding.
An estimated 80 businesses in Newry are counting the cost after the city’s canal burst its banks on Monday night, submerging sections under water.
A Department of Infrastructure official said they still have concerns about Newry, over the impact of high tide potentially causing further breaches of the canal wall.
Gary Quinn from the Rivers Agency said they have placed a large number of sandbags in the city.
“We have a focus on Portadown, we have a focus on Banbridge. The Bann river level is rising, but there are numerous towns and villages where we have had to respond to some more local type impacts,” he told the BBC.
“But our main focus is on Newry and Portadown.”
Newry courthouse has been temporarily closed with business moved to Craigavon
The department of justice said the measure was to allow for remedial works to take place and to make sure the staff and public are kept safe.
“Court business will return to Newry Courthouse as soon as possible,” they added.
Roads and some train services have been disrupted in counties Down, Antrim and Armagh amid rising waters.
On Wednesday morning, public transport authority Translink said the Bangor train line was closed for a period. It has since reopened.
The Department for Infrastructure said it remained on high alert through the night.
It received almost 800 calls to its flooding incident line, and has distributed more than 12,000 sandbags to the areas worst affected.
A spokesperson said river and lough levels continue to be monitored as levels rise and will continue be monitored over the coming days.
“People are urged to stay away from flood defences, flooded areas and watercourses,” they added.
Further rain is expected with the arrival of Storm Ciaran later.
The Met Office has issued a yellow warning for rain for the eastern half of Northern Ireland on Thursday.
In Newry, Paul McCartan, owner of McCartan Bros menswear store, estimated it will cost about £250,000 to repair and restock his shop.
Michael Nugent, owner of Nugelato Ice-Cream Parlour, is still counting the costs but estimated repairing the damage could be up to £100,000.
He said: “This is the first day we have been able to access the shop, with the levels of flooding yesterday it was under a few feet of water. While the water has thankfully left our shop, it has gone down the road and there is still a big problem.
“For our shop, it’s going to be about salvaging what we can.
“We didn’t have much warning, had we known we possibly could have got equipment and stock out.”
Mr Nugent said they have not yet heard of any financial aid that might be made available to businesses.
He added: “We haven’t heard a thing as yet … we have had no assurances. Most businesses in Newry aren’t insured with flood risks.
“We need some leadership and some support.
“If we have to replace everything … it could be upwards of £100,000.”
