Door drop marketing company Link Direct has demanded a right to reply from the BBC, while Two Sides claimed it was "alarmed" at how the paper industry was portrayed.
A spokesman for the BBC told PrintWeek that the Direct Marketing Association (DMA) was given the right to reply in the BBC One show.
He added: "The programme made clear that the overwhelming majority of junk/direct mailers are legitimate.
"However, the damage done by criminal gangs based abroad targeting the vulnerable with scam mail and the ease with which the gangs exploit the Royal Mail's Local Look service is a matter of grave concern and merited being brought to public attention."
However, the DMA criticised Panorama for mixing up so-called 'junk mail' and scam mail in its attempt to report on both in the course of a single half hour programme.
A spokeswoman said: "Panorama confused matters by addressing the unrelated issues of scam mail and the so-called ‘junk mail’ industry. While both are of great concern, the programme addressed both as if they had similar causes, similar effects and should be dealt with in a similar manner.
"Scam mail is a criminal activity that involves unscrupulous con artists fleecing the vulnerable. We unequivocally support the fight against scam mail and works alongside campaigning organisations such as Think Jessica to bring an end to it."
Chris Roxburgh, a director of Birkenhead-based Link Direct has since written to the BBC director general Mark Thompson stating that the 4 July programme misrepresented the industry.
He said: "This programme was fundamentally flawed, clumsy, ill-informed and unbalanced.
"I am demanding from Mark Thompson the opportunity of putting our industry's side of the story as a matter of priority to try to correct the damage this programme has done to a sector that supports 280,000 jobs."
Roxburgh went on to argue that Panorama made a "damaging misjudgement" by crowbarring an insight into junk mail during an investigation into scam mail.
"Our sector has nothing whatsoever to do with scam mail and it is outlandish and deeply damaging to us that we were thrust into the spotlight with this criminal activity," he said.
The show, which was partly filmed in Cornwall, estimated that 4,000 tonnes of junk mail end up in the county's landfill every year. Panorama claimed that - by extension - junk mail costs the UK taxpayer £50m every year – a figure that does not agree with Two Sides' figures on recycling.
Two Sides director Martyn Eustace said: "Yet again the paper and print industry is the victim of misleading reporting. Unwanted mail is of course wasteful and the industry is fully supportive of improvements to data management and targeting which will ensure that the right and relevant mail is delivered to households.
"Paper to landfill is unnecessary - we need the fibre back. Landfill issues are very important and the problem is largely in the collection streams. We can use all the waste paper collected if recycling is improved – zero to landfill is our objective. European recycling rates for paper are close to 70% and the trend shows continuing improvement."
