WASHINGTON, May 30 — Twenty death certificates for Afghan and Iraqi prisoners who died in American custody were completed in a 10-day rush only after the investigation into the notorious abuses at Abu Ghraib became public last month, even though some of the deaths occurred months — in some cases many months — before.
Officers from Dover Air Force Base in Delaware, the headquarters of the Armed Forces Medical Examiner, signed the certificates between May 12 and 21, including one certificate for an Afghan prisoner killed at the American military base at Bagram on Dec. 10, 2002, in what an autopsy found was a homicide.
In the aftermath of the international outcry over the abuses at Abu Ghraib prison, the Pentagon has repeatedly said it thoroughly investigates all accusations of mistreatment and misconduct. But as the handling of the death certificates suggests, many of the known investigations into abuses against Afghan and Iraqi detainees moved glacially, at least until the photographs of hooded, shackled and naked Iraqi prisoners appeared late last month.
According to military officials and a review of Army documents, the investigations have been complicated by a variety of factors, including austere and violent conditions in Iraq and Afghanistan, cultural and language barriers and a convoluted and sluggish military bureaucracy. Many of the witnesses are former prisoners who melted back into society and soldiers who have returned to the United States or redeployed to other countries.
Moreover, only a few dozen military investigators are in Iraq, and they are responsible for examining everything from petty crimes by soldiers to war crimes Iraqi forces committed against Americans during the war.
Some, including lawyers for those accused at Abu Ghraib, have called for a special court of inquiry that would consolidate the investigations and remove them from the military chain of command, which includes commanders whose role in authorizing or creating conditions that allowed abuse to fester.
The abuses at Abu Ghraib have prompted an array of investigations, including one by the Army's inspector general and another by the deputy head of Army intelligence, but each has distinct mandates, limited scope and, to some, inherent conflicts of interest.
"There is already ample evidence of a confusing array of investigations," said Eugene Fidell, the president of the National Institute of Military Justice in Washington. "I believe the situation has already lost focus. It has all the makings of an investigative debacle."
After first giving conflicting accounts, the Pentagon now says that at least 33 investigations have been opened involving 37 deaths of prisoners. There are also an unknown number of investigations into assaults and other abuses. Some of the deaths were attributed to natural causes; others involved prisoners killed in what investigators determined to be justified homicides, like the shooting deaths of four Iraqis during a riot at Abu Ghraib in November.
But even now, officials say they cannot specify how many cases remain under criminal investigation, though the death certificates and an Army summary of cases obtained by The New York Times show that at least 12 cases involving homicides or unexplained deaths of prisoners remain unsolved, 8 in Iraq and 4 in Afghanistan.
The officials acknowledge they are not even sure how many deaths have occurred in American custody. Even before the Abu Ghraib abuses, the International Committee of the Red Cross and human rights organizations reported mistreatment of prisoners, and even deaths, involving American or other troops in Iraq and Afghanistan. It is not clear that those cases are under investigation.
Of the 37 deaths that have been investigated, only one soldier, who has not been identified, has been punished for what was ruled a homicide, according to Army officials and the documents. He was demoted and discharged, but not court-martialed, after fatally shooting a prisoner who was throwing stones at a detention center northwest of Baghdad on Sept. 11, 2003.
In another case, involving the Marine Corps, two marines face court-martial this year in connection with the death of Nagem Sadoon Hatab, an Iraqi who died in a prison camp near Nasiriya last June 6.
The 20 recently completed death certificates were among 23 that the Pentagon released a week ago. It is not clear why there is not paperwork for all 37 prisoner deaths that the Pentagon acknowledges in Iraq and Afghanistan. Officials said that in some cases, though not all, no death certificates had been completed because no autopsy was conducted.
"We also know that it's not the complete picture," a senior Pentagon official said when the documents were released.
A Pentagon spokesman could not explain why the certificates — seven of which classified the deaths as homicides — were completed only this month, but he suggested that it was a bureaucratic oversight that did not affect investigations now under way.
"At the time of the autopsies, the emphasis was on getting an autopsy report out to the investigative agency, not the certificate," the spokesman, James Turner, said in a written response to questions. "Death certificates are a document for society to use. And we had no one to issue a death certificate to in Iraq. We have a mixture of certificates in the case files: some hand-written, some typed, and in some cases, no death certificate."
Nevertheless, the Pentagon has changed its policy and will now complete certificates within two weeks after an autopsy — the same required for any American soldier who dies, Mr. Turner wrote.
The Army's Criminal Investigation Command investigates every death involving Americans, including the deaths of soldiers or of detainees in American custody.
The exact number of the command's agents now in Iraq is classified, but a spokesman, Christopher P. Grey, said it was in the dozens. They are operating outside the chain of command to shield them, in theory at least, from the influence of commanders.
Maj. Gen. Antonio M. Taguba, in his report on the abuses at Abu Ghraib, praised the "superb job" done by investigators who conducted more than 50 interviews with witnesses and suspects after the discovery of photographs depicting the mistreatment there.
Others, however, have raised questions about the Criminal Investigation Command's ability to investigate such complex and delicate cases thoroughly and promptly.
A soldier from 377th Military Police Company, an Ohio Reserve unit, who is being questioned about the deaths of two prisoners in the company's custody in Afghanistan in December 2002, said in an interview that agents interviewed him for the first time in late January or early February, more than a year after the deaths and after the Abu Ghraib investigations began.
Harvey Volzer, a civilian lawyer who represents one of those accused in the Abu Ghraib abuses, Specialist Megan M. Ambuhl, complained that the agents in that investigation had not aggressively asked follow-up questions or pursued investigative trails that would have led to higher-ranking officers.
Documents in the investigation, including a copy of agents' reports, also raised questions. In a list of recommended charges, one suspect is listed simply as an unknown white male with the 372nd Military Police Company from Maryland, even though there was enough evidence to charge him with indecent assault, cruelty and other serious crimes.
In another document, Lt. Col. Jerry L. Phillabaum, commander of the 320th Military Police Battalion, which oversees the 372nd, wrote that he had helped an agent "secure evidence and take sworn statements" even though the accusations were against soldiers under his command and his own actions would, presumably, be under scrutiny. He was later suspended and given a reprimand, but has not been charged with any crimes.
Mr. Grey, like other Pentagon officials, declined to discuss the details of any case, saying that to do so could compromise the investigation. Asked about the length of some of the inquiries, he replied in writing, "Criminal investigations are conducted to a thoroughness standard, not necessarily to a timetable."
He acknowledged that the investigations of two cases in Bagram in December 2002 had recently received new urgency after "additional leads were identified and questions arose that required further investigation." He added that those two cases "are near completion."
"These investigations are not like on TV," he said in a telephone interview. "They're in a combat zone. You can't just jump in a squad car and go interview a couple suspects."
Douglas Jehl, Eric Schmitt and Kate Zernike contributed reporting for this article.