Andy Coulson was cleared for work at No 10 Downing St last year after an investigator who had also done work for News International carried out his vetting.
Coulson, Prime Minister David Cameron's media chief who resigned in January as the phone-hacking scandal developed, was scrutinised by an experienced investigator with strong links to the Security Services, but who also had professional connections with the newspaper group that owned the News of the World, which Coulson had previously edited.
The revelation is certain to renew controversy about Cameron's 2007 decision to appoint Coulson months after the former journalist's resignation as editor of the the paper when two men were sent to prison for phone hacking. The process, which took place around the time of last year's election, gave Coulson the green light to work alongside the Prime Minister in Downing St and to see some secret documents.
Last week, a former tabloid journalist and author, Wensley Clarkson, alleged on Newsnight that the investigator in question - who is known to Clarkson - "would have used phone hacking in the past" as one of his investigative tools.
Now the Independent on Sunday has learned, independently of Clarkson, that the person had done work for News International, a conflict of interest of which the PM is aware and knowledge of which is likely to cause embarrassment in Downing St. A No 10 spokesman said he had spoken to "several top security people" and issued a categorical denial that the work had been "farmed out" to a private investigator, but left open the possibility that someone working for the Security Services had done work for News International.