A senior journalist at Rupert Murdoch's News of the World allegedly paid a private investigator to hack into the computer of a former intelligence officer.
The BBC's Panorama programme, to be broadcast tonight, will claim that the hacking led to the interception of emails in July 2006, when the newspaper was being edited by Andy Coulson, who later resigned as the Prime Minister's communications director.
Mr Coulson, who is not the senior journalist who allegedly commissioned the hacking, has always denied any knowledge of lawbreaking at the title.
According to Panorama, one attempt centred on a former intelligence officer who had sensitive information about an informant in Northern Ireland who was the subject of a court order. Football managers are also said to have been the target of computer hacking.
So far allegations of hacking at the News of the World (NotW) have involved the illegal eavesdropping of mobile phone voicemails. The NotW's royal editor Clive Goodman was jailed alongside a private investigator, Glenn Mulcaire, four years ago for hacking the phones of royal aides.
Scotland Yard has been criticised for failing to follow up leads amid evidence that illegal techniques were more widespread at the paper.
In advance publicity, the BBC said: "Phone-hacking was once dismissed by executives at News International as the illegal work of one 'rogue reporter'... Panorama exposes the extent of the 'dark arts' employed by journalists across the industry to get their story. The programme reveals a dishonourable history of law-breaking that went beyond phone-hacking and questions the police inaction that let it continue."
The private investigator is reported to have gained the confidential information using "Trojan viruses". Once activitated, the viruses – sent in the form of innocuous emails – would allegedly relay confidential data from the computer of a target to private investigators.
The News of the World issued a brief statement saying: "Panorama has produced no evidence whatever to support their allegations, despite several requests from us to do so. As shown by recent events, we will not tolerate misconduct by our staff."
The hacking scandal has deepened with a series of new allegations in recent days. The Labour MP Chris Bryant claimed in the Commons on Thursday that there had been a cover-up into the discovery of thousands of phone numbers of apparent or potential hacking victims.
He also claimed that he had been warned via friends by an ally of Mr Murdoch that raising the issue in Parliament "would not be forgotten".
On Friday The Guardian disclosed that the News of the World reportedly paid a private investigator, Jonathan Rees, £150,000 a year to supply illegal data from a network of corrupt police officers, bank workers and phone company employees.
On Saturday, the Metropolitan Police's acting deputy commissioner, John Yates, wrote a letter to The Independent defending his handling of a review of the first police investigation.
In tonight's Panorama, Brian Paddick, a former Met commander, reiterates his view that his former employer should be stripped of the investigation, which should be handed to an outside force with independent supervision.
Mr Paddick, who suspects that his own voicemail may have been intercepted, said: "Otherwise, certainly some of the victims of phone-hacking will not be satisfied that the thing has been investigated thoroughly."