US government officials may have conspired to conceal evidence that three Guantánamo Bay inmates could have been murdered during interrogations, according to a six-month investigation by American journalists.

All three may have been suffocated during questioning on the same evening and their deaths passed off as suicides by hanging, the joint investigation for Harper's Magazine and NBC News has concluded.

The magazine also suggests the cover-up may explain why the US government is reluctant to allow the release of Shaker Aamer, the last former British resident held at Guantánamo, as he is said to have alleged that he was part-suffocated while being tortured on the same evening.

"The cover-up is amazing in its audacity, and it is continuing into the Obama administration," said Scott Horton, the contributing editor for Harper's who conducted the investigation.

When the three men – Salah Ahmed al-Salami, 37, a Yemeni, and two Saudis, Talal al-Zahrani, 22, and Mani Shaman al-Utaybi, 30 – died in June 2006, the camp's commander declared that they had committed suicide and that this had been "an act of asymmetrical warfare", rather than one of desperation.

According to an official inquiry by the US navy, whose report was heavily censored before release, each man was found in his cell, hanging from bedsheets, with their hands bound and rags stuffed down their throats.

However, Horton spoke to four camp guards who alleged that when the bodies were taken to the camp's medical clinic they had definitely not come from their cell block, which they were guarding, and appeared to have been transfered from a "black site", known as Camp No, within Guantánamo, operated by either the CIA or a Pentagon intelligence agency.

The men said that the following day, a senior officer assembled the guards and told them that the three men had committed suicide by stuffing rags down their throats, that the media would report that they had hanged themselves, and ordered that they must not seek to contradict those reports.

Harper's says that when the bodies of the three men were repatriated, pathologists who conducted postmortem examinations found that each man's larynx, hyoid bone and thyroid cartilage – which could have helped determine cause of death – had been removed and retained by US authorities.

The men's bodes did show signs of mistreatment, however, including bruising and needle marks. Al-Salami's jaw was broken and several teeth missing, injuries that an earlier US pathologist's report attributed to an attempted resuscitation.

Aamer's account of his mistreatment on the same evening as the three deaths appears in papers lodged with a district federal court in Washington. His lawyer, Zachary Katznelson, wrote in an affidavit that Aamer had been beaten for two and a half hours by seven naval military police after he refused to provide a retina scan and fingerprints.

"He reported to me that he was strapped to a chair, fully restrained at the head, arms and legs. The MPs inflicted so much pain, Mr Aamer said he thought he was going to die."

The MPs are also alleged to have pressed on pressure points and held Aamer's eyes open while shining a torch into them. "When he screamed, they cut off his airway, then put a mask on him so he could not cry out," Katznelson wrote.

Aamer, 41, whose British wife and four children live in London, has been held at Guantánamo for almost eight years. Next Friday marks the first anniversary of President Obama's order that the camp be closed within a year, but around 214 other men are also still detained there.

In the days that followed the deaths of the three men, US navy investigators seized every piece of paperwork possessed by other inmates. Harper's reports that when the US justice department subsequently went to court to defend the seizure of correspondence between inmates and their lawyers, the judge commented on one aspect of the department's case: that its "citations supporting the fact of the suicides" were all drawn from media accounts.

Harper's also reports that two of the three men had been due for release when they died, and that family members doubt they would have taken their own lives.

One of Horton's sources, a former staff sergeant in his mid-40s called Joseph Hickman, approached the department of justice via his lawyer in February last year to report his concerns, but Harper's says a subsequent investigation appears to have been shelved, raising concerns that the department had been compromised by its own role in the use of torture in the "war on terror".

"Under George W Bush, the CIA created an archipelago of secret detention centres that spanned the globe, and authorities at these sites deployed an array of justice department–sanctioned torture techniques – including waterboarding, which often entails inserting cloth into the subject's mouth – on prisoners they deemed to be involved in terrorism," Horton says.

"The experience of Sergeant Hickman and other Guantánamo guards compels us to ask whether the three prisoners who died on 9 June were being interrogated by the CIA, and whether their deaths resulted from the gruelling techniques the justice department had approved for the agency's use – or from other tortures lacking that sanction."