Geoff White, a former senior detective, left his post after a police watchdog began the inquiry into allegations surrounding a murder inquiry overseen by him.
The move raises fresh doubts over the Iraq Historic Allegations Team (IHAT), investigating claims that Iraqi civilians suffered illegal treatment at the hands of British forces between 2003 and 2008.
In particular, it raises the possibility of the already long-drawn out investigation taking even longer, meaning soldiers facing further uncertainty over their future.
IHAT has so far identified more than 100 serving and former members of the Armed Forces who it wants to interview about the alleged torture and ill-treatment of civilians, but has brought no charges.
Mr White, who was awarded the Queen’s Police Medal in the 2007 Birthday Honours, was appointed to lead IHAT in autumn 2010 after a police career in which he became head of CID in Staffordshire.
He stepped down without explanation in September, but it can now be disclosed that he left after he was told that the Independent Police Complaints Commission was investigating him – although he denies the two are linked.
Mr White was in charge of Staffordshire Police CID when it investigated the murder of Kevin Nunes, a drug dealer, in 2002. Nunes had been lured to a country lane and murdered by a “firing squad”.
Five men from rival drugs gangs were convicted of murder in January 2008, but the Court of Appeal quashed the convictions earlier this year after it was found that the force had failed to disclose significant evidence to defence lawyers.
The judges said there was a “serious perversion of the course of justice” and called it a “shocking episode”. Those alleged failings are now being investigated by the IPCC. In total, 14 serving and retired police officers are under investigation in an inquiry led by Mick Creedon, Derbyshire’s chief constable.
Last night Simon McKay, a solicitor advocate who represented British soldiers under investigation, said: “If the IPCC conclude that the allegations Mr White faces are made out then this inevitably raises questions about the integrity of other inquiries, including IHAT, that he may have played a role in.”
IHAT is made up of civilian investigators, working under the Royal Military Police. Last year it began taking statements from more than 150 Iraqis who claimed they suffered ill-treatment at the hands of British forces after the overthrow of Saddam Hussein in 2003.
A separate unit of IHAT is examining the results of a previous inquiry into the killing of Baha Mousa, an Iraqi hotel worker who died in British custody in 2003. One soldier has already been jailed over the death.
At least 19 more incidents are being investigated to see whether charges can be brought, with three soldiers suspended from duty in connection with the inquiries.
Patrick Mercer, a Conservative MP and a former infantry officer, said: “There’s no doubt that there were things that went wrong in Iraq, but finding out the full truth is severely hindered by the former head of IHAT having these sorts of accusations hanging over him.”
In a statement, Mr White, 55, said: “I have fully co-operated with the IPCC inquiry, being one of a number of serving and retired officers to have been interviewed by them to date.
“I emphatically deny any wrongdoing or having any knowledge of any wrongdoing. I do not consider it appropriate to say anything more whilst the inquiry is ongoing.
“For the avoidance of doubt, my decision not to renew my contract with the MoD in September was made for reasons entirely unconnected with the IPCC inquiry.”
By David Barrett