A cross-Border body could face a complete breakdown between the North-South elements of the organisation because it has been continually dogged by controversy, it was claimed in the Dáil.
Dinny McGinley (FG, Donegal South West) alleged that staff in the Republic's section of Waterways Ireland were paid more than their counterparts in the North for the same sort of work and responsibilities. He said serious allegations of bullying had been upheld and there was mismanagement and malpractice in appointments made to the organisation that "could do serious damage to North-South relations".
Minister for Community, Rural and Gaeltacht Affairs Eamon Ó Cuív said, however, that Waterways Ireland, responsible for inland waterways across the island, "has an excellent record in managing its core business".
He added that the bulk of the allegations were not upheld by independent investigators.
Mr McGinley, who has raised the all-Ireland organisation in the Dáil on a number of occasions, said Waterways Ireland was becoming a regular topic of conversation in Westminster as well as the Dáil.
Serious charges of bullying had been upheld, Mr McGinley said, and "appointments to senior positions that should have been publicly advertised for open competitions had proceeded without adherence to the procedure in spite of undertakings given in Stormont in 2002" that there would be open and publicly advertised competition.
He said: "Serious claims have been made of discrimination in these appointments on grounds of religion, politics and nationality, which would be disastrous if found to be true."
Mr McGinley said that one individual had applied to the Fair Employment Tribunal in the North.
"In spite of the best efforts of Waterways Ireland, this case is being processed and heard at the moment," he said.
The Fine Gael TD believed that "being continually dogged by such controversies will do no service to us here or our people in Northern Ireland". Mr Ó Cuív said, however, that the serious charges made had been independently investigated and the bulk of allegations "were not upheld by the investigation. That is a matter of fact."
A report by the investigators nonetheless had recommended that a number of actions be taken by the organisation "and all the agreed actions have now been delivered upon by the CEO" and the Government departments North and South "are satisfied that this brings the matter to closure".
He said one of the people with a grievance who was part of the investigation had taken a case for his dismissal and was seeking reinstatement, as was his right. Waterways Ireland would defend itself and its action in that case, "particularly based on the investigators' report".
Asked about employees in the South being paid more than those in the North for similar work, Mr Ó Cuív said he would seek an explanation but "marrying two jurisdictions with different rates of pay and different tax systems poses its challenges".