Earlier in the week, Panorama aired evidence alleging that NDS had hacked into the technology used by ITV Digital - a key rival to News Corp's Sky in the early 2000s - and then made the data freely available to pirates.
However, NDS has now claimed that Panorama "seriously misconstrued legitimate activities" in a programme that was "misleading and deeply damaging" to NDS and Rupert Murdoch's News Corp.
The pay-TV smartcard firm claimed that the programme showed a "flagrant disregard to the BBC's broadcasting code" and also misled viewers with "widespread misreporting". It demanded that the BBC retraced the allegations 'immediately".
News Corp itself has also accused the BBC of "gross misrepresentation" over allegations made in the broadcast on BBC One on Monday.
In a letter to Panorama producer Alistair Jackson, NDS executive chairman Abe Peled said that the programme featured "manipulated emails" to support its claims that NDS waged a hacking and piracy campaign to weaken On Digital, later ITV Digital.
Panorama's clams were based on the evidence of Lee Gibling, who set up a website in the late 1990s referred to as 'The House of Ill-Compute', or Thoic.
After information on the ITV Digital cards - made by Canal+ - was stolen by a hacker, Gibling told the BBC that he was paid to make the data widely available via Thoic, overseen by Ray Adams, who at the time was head of UK security for NDS.
Adams denied any knowledge of the ITV Digital code, but internal NDS emails appeared to show that the hacked code was passed to him by a technology expert at the firm.
But Peled maintains that key emails featured on the programme were actually part of anti-piracy work by NDS. He said that the BBC manipulated the emails to hide that they were forwarded to Adams from Thoic by an undercover agent working for the firm.
"Despite your on-air claims, this manipulated email is not evidence of NDS promoting or facilitating piracy," said Peled in his letter to Jackson.
"To the contrary, in its original form, this exchange is clear evidence of NDS's ongoing anti-piracy activities. Furthermore, you displayed total flagrant disregard for the true context surrounding emails cited."
He continued: "For example, you purported that an email sent to Ray Adams was evidence of NDS's encouragement of piracy associated with the thoic.com website.
"That email, however, was sent from an undercover agent at thoic to NDS, not from NDS to thoic. Thoic was a website on which any user could post information.
"The email, in its original form, cannot reasonably be interpreted as evidence of NDS's participation in or promotion of piracy. Instead, it is further proof of NDS collecting information from thoic as part of its long-standing fight against piracy."
Peled claims that Panorama has ignored requests to "identify the factual allegations" made against his firm, and said that this is part of a wider campaign to discredit NDS and News Corp.
"Were you to have shared this manipulated and misleading material with us prior to broadcast, we would have shown you that this cache of stolen emails had been obtained and manipulated as part of an ongoing plan by third parties to damage the reputation of NDS, our sister companies, and News Corporation," his letter said.
"Frankly, it is outrageous that Panorama has facilitated these actions by third parties to damage our name. We look forward to your swift response and resolution of this matter."
Yesterday, News Corp's chief operating officer Chase Carey also hit out at the BBC's claims against NDS, saying that the programme "presented manipulated and mischaracterised emails to produce unfair and baseless allegations".
The response from News Corp and NDS comes after further allegations emerged against the firms in the Australian Financial Review, which said that a campaign of piracy was also waged to weaken rival Australian pay-TV operators such as Austar and Optus.
Carey said that the report, along with an investigation by PBS Frontline in the US, had "piled on - if not exaggerated - the BBC's inaccurate claims".
News Corp jointly owns NDS with private equity group Permira, but recently agreed to sell the business to Cisco on a planned $5bn deal.
NDS has fended off four legal actions over the past decade from pay-TV companies, although only the case of Echostar actually went to court in the US.
Carey said that News Corp "supports NDS in clearing its name".