Mark Daly: A new inquiry into these corruption allegations is needed to answer lingering questions

"The smell of corruption was there. Yes, we rather regretted that we couldn't get more evidence," Dr Richard Stone, the right-hand man to Sir William Macpherson told me in 2006.

His comments came seven years after Sir William's historic Stephen Lawrence Inquiry in a controversial BBC film, which revealed that a corrupt policeman – former Det Sgt John Davidson – might have hampered the investigation into the black teenager's murder. This was based on the testimony of Neil Putnam, a corrupt cop turned supergrass, who had been trusted by the Metropolitan Police and the Crown Prosecution Service to implicate and convict five of his and Davidson's bent colleagues.

Not only did he allege that Davidson had been paid by Clifford Norris, the father of one of the Lawrence killers, but also that he had told this to his police debriefers when he turned – and that he thought the Met had suppressed it. It was a toss-up which was the most serious allegation, both being incredibly damaging for the Met.

The Met furiously denied the claim. The ensuing IPCC investigation concluded there was no evidence to support our film and the Met launched a blistering attack on the BBC's journalism, accusing it of sensationalism and "utterly outrageous" film-making. This week to its great credit, The Independent has published fresh evidence supporting Neil Putnam's allegations.

Tuesday's Independent revealed that in a recent court case, Putnam provided testimony to the Old Bailey about John Davidson's alleged confession that he was in league with Norris. He also repeated what he told the BBC – that he'd told the Met about it in 1998 and wanted the information to be passed to the Macpherson inquiry. It never was.

It was also revealed that a former CPS barrister told the same court he'd been aware of this alleged link between Davidson and Clifford Norris. A second lawyer from the Met recollected a similar story.

Wind back, to 2006, when I was interviewing Assistant Commissioner John Yates over these claims. Yates had headed the Met's CIB3 team, which investigated corruption in the ranks. He told me Putnam was "astonishingly brave ... a credible witness, and a witness of truth" in all the other corruption claims he'd made – but not on the Davidson/Norris connection. "On this point he is mistaken," Yates told me, although he admitted that he was certain Davidson was an otherwise bent cop. Putnam was outraged, knowing the Met had used his testimony to imprison another five corrupt cops. Davidson has always denied being corrupt.

Putnam said: "At the time I wasn't wrong about anything else, I didn't lie about anything else. No, they [the Met] thought I was a witness of truth." Putnam alleged the Met had suppressed the allegation, made whilst the Macpherson inquiry was sitting, "to protect the Metropolitan Police."

I know Neil Putnam, a born-again Christian, did not take lightly the decision to give me an interview for The Boys Who Killed Stephen Lawrence. He himself had been corrupt, and had served a three-year prison sentence. He knew he'd come under fire, and likely be the subject of further investigations. But he said he felt compelled to do it because of the injustice suffered by the Lawrence family. The strain of the programme and its ramifications eventually told on Neil, and I believe may have contributed to the eventual breakdown of his marriage. It was a high price to pay, and I admired his having the courage to come forward.

I had hoped it would be worth it. In the face of such vigorous denials from Yates, I couldn't get to the bottom of Putnam's claims and was pleased that the IPCC had launched its investigation. With all of its regulatory powers I hoped it would be able to access sensitive police documents I could not. The IPCC inquiry was a disappointment to me, leaving me wondering firstly about its grasp on the detail of what admittedly is a labyrinthine case; but secondly whether it had indeed managed to access all of the key information.

The IPCC did unearth some testimony from the two lawyers mentioned previously which seemed to bolster Putnam's claims, but attached little significance to that, concluding there was "no evidence" to support Putnam's or the BBC's allegations.

I now understand the IPCC saw five notebooks from Putnam's debriefers, which contained no trace of his Lawrence claim. The Met says there were only ever five. Yet Putnam told the court there were at least 15. If he's right, that means there are 10 missing notebooks the IPCC didn't get to see. The IPCC stands by its report.

Putnam's recent court appearance came during a CPS attempt to re-try two of the five men initially convicted in 1999 in a case previously described as the jewel in CIB3's crown. However, at the Old Bailey, CIB3 techniques came under increasing scrutiny and it emerged prosecutors had failed to disclose large bundles of documents. Putnam and his fellow supergrass also alleged in court they had been unfairly pressurised by Yates's team in debrieings, which, incredibly, were not tape-recorded. The case collapsed. It is expected that other convictions secured by CIB3 will come under fresh scrutiny and may be overturned.

Yates has of course now left the Met. He has come under regular and intense scrutiny at Leveson over his role in the phone-hacking scandal and claims of relationships with journalists. The legacy of CIB3 has also come under serious question.

In light of this week's developments there have been fresh calls for a new Lawrence corruption inquiry. I would welcome that. So would Dr Stone. And most importantly, so would the family of Stephen Lawrence who, more than anyone, deserve more answers to this painful, long-running saga than they have so far been given.

Mark Daly is the investigative reporter behind the BBC's 2006 film "The Boys Who Killed Stephen Lawrence" and this year's "Panorama: Stephen Lawrence – Time for Justice"