Several major cases - including claims that an RAF prisoner was beaten to death and a taxi driver was shot dead - have been closed because not enough independent witnesses could be found.
It is estimated that up to half of the 14 cases of alleged murder and serious abuse of Iraqi civilians by British troops which have been referred to military prosecutors have been dropped or are close to collapse.
The disclosures come in the week that seven British soldiers, including a colonel, were charged over the death in custody of the Iraqi hotel receptionist Baha Mousa - a case revealed by The Independent on Sunday.
The Attorney General, Lord Goldsmith, said three Queen's Lancashire Regiment soldiers had been charged under war crimes legislation. The QLR's then commander, Colonel Jorge Mendonca, faces negligence charges.
Lord Goldsmith also announced manslaughter charges against four Irish Guardsmen after a prisoner drowned when they allegedly beat him and forced him to swim a canal in May 2003.
But these announcements have overshadowed an increasing number of cases that have collapsed or been discontinued - deepening concerns in senior legal circles about the ability of the military police and prosecutors to handle complex and serious cases.
Ministers have repeatedly insisted the military legal system is robust and independent, but prominent lawyers, including the human rights lawyer Phil Shiner, and opposition MPs claim the system is deeply flawed. Mr Shiner said: "The fundamental problem is that the military is investigating and prosecuting itself. Time and time again, cases collapse or take years to come to court."
The pressure on John Reid, the Secretary of State for Defence, and Lord Goldsmith to introduce sweeping reforms of military investigations is now intense. Earlier this month, ministers came under attack on another front when six former chiefs of the defence staff, now in the House of Lords, accused the Government of "political correctness" and caving into political pressure by prosecuting some soldiers unfairly.
The criticisms focus on concerns that the military police are too ill-equipped to investigate complex cases effectively and that military lawyers are involved in cases far too late in the inquiry. As a result, evidence and witnesses are often too weak to be used.
However, the Ministry of Defence says it plans wide-ranging reforms in the Armed Forces Bill later this year, which will introduce a single military prosecutor and courts martial system, and a single system of service law.
The dropped cases include:
* In March, manslaughter charges were dropped against a soldier who allegedly shot dead an Iraqi taxi driver whose car door accidentally hit him in April 2003. Military police failed to get enough independent witnesses. The MoD now admits "there is no realistic prospect of successful prosecution".
* Prosecutors may drop manslaughter charges against three men from the 32 Engineering Regiment after they allegedly threw a suspected looter into a well as a punishment in May 2003. He drowned. Ministers admitted in January there was "substantive evidence of deliberate abuse in custody", but there are problems finding enough independent Iraqi witnesses.
* A case against three members of the Royal Air Force Regiment suspected of beating an Iraqi prisoner to death on a helicopter in April 2003 were dropped several months ago. An anonymous phone caller said the prisoner was killed by "three RAF personnel by beating and kicking". Again, few witnesses willing to go to court could be found.
* Manslaughter charges against a Trooper Ahern for allegedly shooting dead an Iraqi in May 2003 while on guard duty were dropped because the teenager was on his first combat tour and there were doubts over the precise circumstances of the shooting.Reuse content