Large parts of the Co Down town remained under water on Saturday after heavy rainfall earlier in the week swamped many businesses.
Newry, Kilkeel and Portadown were also badly affected by flooding that hit the north east of the island of Ireland.
Calls continue to mount for significant financial aid to be made available for those counting the costs of the deluge.
Many of the business owners affected had previously been unable to get insurance cover for flood damage.
The powersharing impasse means there are no elected ministers in place at Stormont to take the lead on the response to the floods.
The pumping operation undertaken by the Northern Ireland Fire and Rescue Service began on Friday evening and continued overnight.
A Department for Infrastructure statement said: "This is a complex operation which used two high volume pumps moving in excess of 7,500 litres per minute using twin six-inch hoses to the discharge point into the Quoile River at the Belfast Road bridge almost a mile away.
"As waters receded, pumping paused temporarily to relocate pumps closer to the low point.
"Water levels in the Quoile are on the decline and monitoring of water levels both in Market Street and the River still continue.
"Market Street and other roads in the area remain closed to facilitate the pumping main. We would appreciate road users to follow the necessary safety messages and diversion routes."
The department said it was not possible to give an exact time frame when the pumping operation would be completed.
"We understand this is incredibly difficult for residents and businesses impacted and we appreciate their patience as we work with partners to manage the situation," the statement added.
"Newry, Mourne and Down District Council has already started to assist businesses, where possible, with the clear-up and is ready to commence a clean-up operation in the town centre as soon as it is feasible to bring large vehicles and equipment onto the streets."