As editor of the News of the World Rebekah Brooks was confronted with evidence that her paper's resources had been used on behalf of two murder suspects to spy on the senior detective who was investigating their alleged crime.

Brooks was summoned to a meeting at Scotland Yard where she was told that one of her most senior journalists, Alex Marunchak, had apparently agreed to use photographers and vans leased to the paper to run surveillance on behalf of Jonathan Rees and Sid Fillery, two private investigators who were suspected of murdering another investigator, Daniel Morgan, when the latter was a partner of Rees's in the firm Southern Investigations. The Yard saw this as a possible attempt to pervert the course of justice.

Brooks was also told of evidence that Marunchak had a corrupt relationship with Rees, who had been earning up to £150,000 a year selling confidential data to the News of the World. Police told her that a former employee of Rees had given them a statement alleging that some of these payments were diverted to Marunchak, who had been able to pay off his credit card and pay his child's private school fees.

A Guardian investigation suggests that surveillance of Detective Chief Superintendent David Cook involved the News of the World physically following him and his young children, "blagging" his personal details from police databases, attempting to access his voicemail and that of his wife, and possibly sending a "Trojan horse" email in an attempt to steal information from his computer.

The targeting of Cook began following his appearance on BBC Crimewatch on 26 June 2002, when he appealed for information to solve the murder of Morgan, who had been found dead in south London 15 years earlier. Rees and Fillery were among the suspects. The following day, Cook was warned by the Yard that they had picked up intelligence that Fillery had been in touch with Marunchak and that Marunchak agreed to "sort Cook out".

A few days later, Cook was contacted by Surrey police, where he had worked as a senior detective from 1996 to 2001, and was told that somebody claiming to work for the Inland Revenue had contacted their finance department, asking for Cook's home address so that they could send him a cheque with a tax refund. The finance department had been suspicious and refused to give out the information.

It is now known that at that time, the News of the World's investigator, Glenn Mulcaire, succeeded in obtaining Cook's home address, his internal payroll number at the Metropolitan police, his date of birth and figures for the amount that he and his wife were paying for their mortgage. All of this appears to have been blagged by Mulcaire from confidential databases, apparently including the Met's own records.

Mulcaire obtained the mobile phone number for Cook's wife and the password she used for her mobile phone account.

Paperwork in the possession of the Yard's Operation Weeting is believed to show that Mulcaire did this on the instructions of Greg Miskiw, the paper's assistant editor and a close friend of Marunchak.

About a week later, a van was seen parked outside Cook's home. The following day, two vans were seen there. Both of them attempted to follow Cook as he took his two-year-old son to nursery. Cook alerted Scotland Yard, who sent a uniformed officer to stop one of the vans on the grounds that its rear brake light was broken. The driver proved to be a photojournalist working for the News of the World. Both vans were leased to the paper. During the same week, there were signs of an attempt to open letters which had been left in Cook's external postbox.

Scotland Yard chose not to mount a formal inquiry. Instead a senior press officer contacted Brooks to ask for an explanation. She is understood to have told them they were investigating a report that Cook was having an affair with another officer, Jacqui Hames, the presenter of BBC Crimewatch. Yard sources say they rejected this explanation, because Cook had been married to Hames for some years; the couple had two children, then aged two and five; and they had previously appeared together as a married couple in published stories."The story was complete rubbish," according to one source.

For four months, the Yard took no action, raising questions about whether they were willing to pursue what appeared to be an attempt to interfere with a murder inquiry. However, in November 2002, at a press social event at Scotland Yard, Brooks was asked to come into a side room for a meeting. She was confronted by Cook, his boss, Commander Andre Baker, and Dick Fedorcio, the head of media relations. According to a Yard source, Cook described the surveillance on his home and the apparent involvement of Marunchak, and evidence of Marunchak's suspect financial relationship with Rees. Brooks is said to have defended Marunchak on the grounds that he did his job well.

Scotland Yard took no further action, apparently reflecting the desire of Fedorcio, who has had a close working relationship with Brooks, to avoid unnecessary friction with the News of the World. In March Marunchak was named by BBC Panorama as the News of the World executive who hired a specialist to plant a Trojan on the computer of a former British intelligence officer, Ian Hurst.

Rees and Fillery were eventually arrested and charged in relation to the murder of Morgan. Charges against both men were later dropped, although Rees was convicted of plotting to plant cocaine on a woman so that her ex-husband would get custody of their children, and Fillery was convicted of possessing indecent images of children.

Cook and his wife are believed to be preparing a legal action against the News of the World, Marunchak, Miskiw and Mulcaire. Operation Weeting is also understood to be investigating.

• This article was amended on 8 July 2011. Wording in the original suggested that at the time Daniel Morgan was murdered, Sid Fillery was among his partners in a private investigations firm. This has been corrected.