Mr Jones, who resigned from Parliament to take up a role as an economic ambassador to the Pacific, this morning declined to comment and directed the Herald to Labour's Commerce spokesman Clayton Cosgrove.
Commerce Commission chief executive Brent Alderton said the allegations were serious and the commission had undertaken an extensive and thorough investigation.
Along with Mr Jones' complaint, about 90 others had been received.
Apart from the retrospective payments issue, the commission also investigated allegations that Progressive underpaid invoices from suppliers by unilaterally claiming early payment discounts it was not entitled to.
The commission also investigated what Mr Alderton called "conduct affecting retail markets", including claims Progressive refused to accept price rises from suppliers and that it unfairly favoured its own freight company over rivals.
Mr Alderton made it clear that he was not saying there was nothing to the 90 complaints the commission received.
"What I'm saying is there was evidence produced, that evidence did not suggest a breach of the Acts."
In its findings on alleged demands for retrospective payments the commission said Progressive had "assertively" communicated its expectations for improved performance and margin from two suppliers and advised it "may have to consider how it sourced, ranged, displayed and promoted" the suppliers' products "if the suppliers failed to meet Progressive's expectations".
The report found that Progressive's analysis of the difference between the actual financial performance of the suppliers' products and what it expected was termed an "ask".
The suppliers told the commission they were initially confused as to whether the "ask" was a request from Progressive for a lump sum payment or other compensation.
"However, the initial confusion was resolved with subsequent communications, and neither supplier felt coerced by improper threats of commercial sanction to concede to Progressive's requests."
While the two suppliers would have felt commercial pressure to improve their performance during their discussions with Progressive, "the evidence does not suggest that this pressure amounted to coercion."
Progressive Enterprises managing director Dave Chambers said his team was very pleased the matter was finally over.
"The shadow of these false allegations has been distracting, but what's really important is that our team has risen to the challenge and worked hard to win back the confidence of our customers. This company is full of hard-working New Zealanders who just want to do the best job they can."
Mr Chambers said his company negotiated "in a competitive environment to bring lower prices to customers, but that it always negotiated in good faith and in a fair and transparent manner".
"Overwhelmingly, we have good working relationships with the 4000 suppliers we partner with across New Zealand."
"In all of the work we did as a business to respond to the commission's investigation, we also saw no evidence at all of what was alleged. If there are improvements that can and should be made as part of this process, then we'll carefully look at those, particularly if they benefit our customers and our working relationship with suppliers."
"We hope some lessons can be learned about the damage false allegations made under parliamentary privilege can cause. It's not how any New Zealander wants to operate and our door is always open for anyone to discuss issues directly with us."
Read the full Commerce Commission report here:
Read Countdown's statement following the investigation findings here:
