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The commission is set to launch an official investigation into the Labour MP's claims that Woolworths-owned Countdown has demanded retrospective payments from suppliers to ensure ongoing access to its supermarket shelves.
In the latest in a series of attacks on Countdown launched from under the cover of parliamentary privilege, Mr Jones suggested Mr Waters was "calling New Zealand suppliers and discouraging them from participating in this legal process lest they face dire consequences in his supermarkets in Australia".
Mr Waters, an Australian who made his name as chief executive of New Zealand's Fletcher Building, fired back quickly.
"I completely reject Mr Jones' allegations and find his insinuations highly offensive. My contribution to business in New Zealand speaks for itself.
"I am extremely disappointed in Mr Jones' behaviour. Attacking an individual and business through the Parliament is no way for any politician to deal with an issue of concern or engage with the business sector."
Mr Jones is facing increasing calls to provide proof of his claims and to make them outside Parliament where he would not have protection from defamation action by Countdown.
Economic Development Minister Steven Joyce said his attack on Mr Waters was "quite a slur on somebody's name".
"Shane has probably gone a fair way further than he needed to go to get these questions put in front of the Commerce Commission and I think he's basking in the political glory."
However, Mr Jones went on to make even more allegations, again in Parliament, claiming Prime Minister John Key had "secret meetings" with Mr Waters and "came home empty handed from a meeting with one of the most powerful commercial men in Australia and New Zealand".
Yesterday, Mr Key dismissed that, saying the only meeting he had with Mr Waters during his trip to Australia last month was at a function at Prime Minister Tony Abbott's official residence with hundreds of other people.
Meanwhile, Campbell Live last night reported claims from a supplier that Progressive Enterprises' employees were paid cash incentives for preferential treatment. The programme said it had been given an affidavit by "a long-time supplier to New Zealand supermarkets".
In the affidavit the supplier said: "I have personal experience of paying Progressive Enterprises Ltd's employees cash incentives."
The payments were made to individuals employed by the company. "I would pay our buyer - the PEL employee with which our company had a business relationship - $500 cash per week.
"Talk of kickbacks were common within the supplier industry."
In a statement to Campbell Live, the company said: "While we've not seen the document referred to, we would encourage this person to take their allegations to the appropriate authorities, including the police.
"We take all allegations of misconduct seriously and have a code of conduct which each of our employees must meet as part of their employment terms."
Countdown continues to "categorically" deny Mr Jones' allegations and says it will co-operate fully with the Commerce Commission.
- Adam Bennett of the NZ Herald