The deputy head of the criminal investigation into the Hillsborough disaster has stepped down from his role following the launch of a corruption inquiry and claims that a high-ranking detective allowed an unauthorised bugging operation at England’s second largest police force.

Assistant Chief Constable Terry Sweeney is the most senior figure from Greater Manchester Police (GMP) to be investigated as a result of whistleblower claims of "cronyism" among top officers and the alleged failure to follow correct procedures or investigate complaints properly.

The Independent Police Complaints Commission (IPCC) said it had launched three inquiries into the actions of a number of GMP staff including the suggestion the force misled the families of victims of serial killer Harold Shipman as well as the public over the secret disposal of human tissue samples.

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The second probe will examine the activities of an unnamed Detective Chief Inspector who it is claimed ordered the bugging of one of the force’s offices as well as allegations that the officer’s actions may have put public safety at risk.

The police watchdog is also investigating claims made by a serving officer that sex abuse allegations were poorly handled and that alleged failings by GMP were covered up.

It is understood ACC Sweeney, a former head of GMP’s Professional Standards Branch, will feature as part of all three IPCC inquiries.

One of the force’s most respected officers, he was a senior figure in the still ongoing inquiry into the suspected poisoning deaths at Stepping Hill hospital as well as being charged with examining reports that GMP officers attended demonstrations organised by the British National Party.

ACC Sweeney also acted as a spokesman during Operation Windermere, one of the largest ever inquiries into alleged child sexual exploitation.

The IPCC announcement comes just two weeks after Home Secretary Theresa May ordered a major inquiry into undercover policing following the publication of a report that found Scotland Yard spied on the family of murdered teenager Stephen Lawrence.

Assistant Commissioner Jon Stoddart, who is leading Operation Resolve, which was launched following the publication of the Hillsborough Independent Panel’s damning report in 2012, said the allegations related to ACC Sweeney’s role at GMP and that he had now returned to his role at the force.

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“I have taken steps to inform the Hillsborough families and other interested parties of recent developments. I and my team remain absolutely committed to supporting the forthcoming Inquests into the deaths of 96 Liverpool supporters at Hillsborough Stadium on 15th April 1989,” he said in a statement.

Operation Resolve is tasked with helping the coroner to decide whether the deaths of the football fans were unlawful. The inquest is due to begin at the end of this month.

IPCC Commissioner Jan Williams said: “These are serious allegations and the gravity and nature of the allegations, and the fact that they are made against senior officers within the force, means they must be investigated independently.”

The first inquiry by the police watchdog will focus on human tissue believed to include organs taken from the exhumed bodies of 12 of Harold Shipman’s victims and retained for more than a decade by police in case of an appeal by the killer or his family before being secretly destroyed.

GMP Chief Constable Sir Peter Fahy said the decision had been taken to spare the families who had lost loved ones further anguish. Sir Peter said decisions surrounding the Shipman investigation were “complex and sensitive”.

He said AC Sweeney had voluntarily decided to step down from his work with Operation Resolve. “This is a personal decision made as he does not want the matter to distract from the operation's important work,” he added.

It is believed the other two IPCC inquiries relate to events which happened within the past five years. Police have confirmed that the unauthorised bugging of a GMP office took place, the watchdog said.