NI Water paid a meter installer £111,000 (€134,159) for undertaking 12,000 appointments where no work could be carried out due to faulty instructions from the public company.
The Stormont Public Accounts Committee said it was "dismayed" to learn that 40% of all installation visits made by the contractor in the period examined were aborted due to errors in information provided by NI Water.
"The total number of meters installed was 18,000; this equates to two abortive visits for every three installations," the PAC report stated.
"It is difficult to understand how NI Water put itself in a situation where it paid this amount of public money for work not to be done."
This weakness in contract management by NI Water, which was first identified in 2010, was outlined in a wider PAC examination of the way an internal fraud investigation was carried out.
The PAC report identified "serious failings" in how the NI Water probe into potential 'invoice slicing' was handled.
Slicing is a practice whereby a contractor's bill is broken down into a number of smaller ones, which each fall below a value threshold where higher level of scrutiny kicks in.
The internal investigation found no evidence of fraud but did identify weakness in contract management.
The PAC report focused less on the initial fraud allegation than the issues with the subsequent investigation.
It found it did not dig deeply enough and senior management were too quick to close down the investigation based on inadequate and incomplete evidence.
The committee also looked at another internal investigation by a public body - this time conducted by the Department for Regional Development's Roads Service.
Members examined whistleblower allegations that favouritism had been shown to one contractor over the purchase of road signs and claims the way the tenders were evaluated left the department open to perceptions of partiality.
PAC chairwoman Michaela Boyle said: "In the case of the whistleblower's allegations against Roads Service staff on the purchasing of road signs, we found that it was a shoddy and incompetent investigation.
"It is hard to avoid the impression that the Department did not have the appetite to get to the truth."
She added: "We were concerned that there was an intolerable delay in investigating the allegations. We were also shocked that over a period of several years, some orders which should have been given to the whistleblower's firm were given to his main competitor, and found it hard to avoid the conclusion that something other than simple error was at play.
"The Committee admires the whistleblower's dogged determination, over many years, to get to the truth, despite the stress that it has caused him, his family and employees."
In regard to the NI Water and Roads Service investigations, both of which have been the subject of earlier Audit Office examination, Ms Boyle said: "Both of these cases point to fundamental weaknesses in fraud investigation practice. These deficiencies can only be addressed by ensuring investigations are led by professional investigators with an understanding of relevant laws.
"The poor quality of these investigations supports the case for establishing a single public sector fraud investigation service."
A spokeswoman for NI Water said: "In keeping with normal protocols, it is inappropriate to comment on reports of this nature.
"NI Water would note however, that this report relates to matters which arose in early 2010 in the context of the PAC report into procurement governance in NI Water at that time. All relevant recommendations arising from that report have already been implemented by the company."