Northern Ireland Water was formed in 2007
Northern Ireland Water has begun contacting thousands of non-domestic customers who were overcharged.
Over 5,000 businesses, farms, schools, charities or churches paid too much - some by as much as £4,000 in a mistake discovered late last year.
A further mistake 2,400 customers may have been undercharged - they will only have to pay back half of what they owe.
"NI Water will be dealing with each individual customer to arrange a refund," said a spokesman.
The mistake is expected to result in a loss of revenue of about £250,000.
Customers were overcharged between £11.70 and £4,206.88. The range of undercharge was £2.83 to £3,063.22
The problem began around the time Northern Ireland Water was formed in 2007 - incorrect data was passed from the old Water Division to the new publicly owned company.
"The original data they got from the Water Division clearly wasn't robust enough - the managers in Northern Ireland Water should have known that," said Fred Cobain, chairman of the Regional Development Committee.
"All of these problems actually emanate from that and we've been discussing this with them for about a year and a half.
"If water charging goes live for domestic customers and the data is the same, which it will be, we could again have significant problems with regards to bills, which would be horrendous."
The SDLP's Tommy Gallagher said: "The whole Northern Ireland Water charging system is a complete disaster.
"The present administration at Stormont went ahead and brought in charges for businesses and community facilities in 2008, without having any ideas who owned certain properties and who they needed to charge."
Last year Northern Ireland Water underestimated its forecasted revenue by £20m.
The mistake, if left unchecked, would have resulted in every household facing £30 extra on their water bill.
The company's then chief executive, Katherine Bryan, subsequently resigned.
Domestic water charges in Northern Ireland have been deferred by the Executive for another year.