Obama signaled a change from Bush-era impunity with an uplifting promise in his first address to the US Congress in February that "America does not torture". When the US state on its own publicizes the seedy and illegal deeds of its agents under a previous administration, it is an indicator that a new beginning is being planned and the ground is being laid for an overhaul of the means through which American national security is pursued.

The Justice Department memos confirm unambiguously the full horror of former US vice president Dick Cheney's claim that protecting national security was a "tough, mean, dirty, nasty business". The CIA's torture chambers spread across the world under the "war on terror" probably witnessed much worse than all of Cheney's adjectives convey.

Bits of information began trickling out soon after Obama's inauguration in January about some of the wrongs of the past committed by the US military-intelligence complex. The first major disclosure to emerge once Obama came to power was about alleged corruption by senior US army officers in Iraq's gigantic reconstruction scam.

An American arms dealer informed US authorities during Bush's reign that "tens of thousands of dollars" were stuffed into pizza boxes and paper sacks and delivered secretly to American contracting offices in Baghdad manned by colonels. Predictably, the lead was suppressed as long as Bush was in charge. As soon as Obama took office, it was reported that federal authorities were "taking a fresh look" at the allegations.

Earlier this week, a US army sergeant was convicted of murder for executing four bound and blindfolded Iraqi detainees and dumping their bodies into a canal in Baghdad in 2007. Court martial proceedings are usually kept wrapped in secrecy and verdicts are not covered by the media like regular civilian proceedings, owing to the principle that the army's morale and image would suffer if its dirty linen was washed in public.

But the fact that the Obama administration allowed this verdict delivered by US military judges in Germany to be announced widely through the news media within the US and abroad is again a pointer to its intentions to clean up the jetsam floating around from the Bush legacy.

Historically, justice has often been trumped by politics on the question of culpability of the US military in overseas wars. When the My Lai massacre of 1968 in Vietnam came to light, the court martial of Lieutenant William Calley was widely covered in the American media as another nail in the coffin of a deeply unpopular war. Yet, hardly three years into his long sentence, Calley was pardoned and set free by the Richard Nixon administration in 1974.

Recent inquiries have shown that Calley was a mere fall guy for My Lai because the massacre which killed more than 500 Vietnamese civilians was an illegal operation planned and coordinated at task force level by a lieutenant colonel-rank official in the US Army.

The American military's internal inquiry that was hidden from public view concluded that 30 senior officers were negligent and 14 were charged with crimes. Neither Nixon nor any succeeding US administrations had the political will to reopen this denial of justice. Obama's commitment to let the truth come out is praiseworthy in light of the obfuscating history of American presidential behavior towards the criminal misconduct of the military in wars.

Some human-rights and legal experts are criticizing Obama for not taking the Justice Department's torture memos further and prosecuting specific CIA agents who committed the abuses on detainees. The International Commission of Jurists has announced disapproval of the blanket amnesty by saying that "without holding to account the authors of a policy of torture and those executing it, there cannot be a return to the rule of law". The perception that the perpetrators of degrading practices in the "war on terror" are getting off without punishment is valid, but it lacks an appreciation of the political minefield that Obama is navigating.

Shortly after Obama's inauguration, a chorus of political and media voices welled up that the "war crimes" of Bush and his neo-conservatives should be prosecuted or fully accounted for through a "Congressional Truth Commission". Obama shot down these balloons by holding that "I'm more interested in looking forward than I am in looking backwards". He expressed a similar sentiment when confronted with calls to sanction prosecution of the CIA's torturers by saying, "This is a time for reflection, not retribution."

Obama's philosophy of uniting rather than dividing Americans, as well as the pragmatic requirement of Republican support for his budget and economic crisis management, were factors in turning down radical demands for bringing all Bush-era culprits to book.

But if the Justice Department memos and the muckraking on the US military's indiscretions in Iraq are considered, Obama is not covering up the ugly past either. During his recent trip to Turkey, he made a significant comment that "moving the ship of state is a slow process as this particular ship is like a tanker, not a speedboat". The message was that he was trying, but the machinery of the American state and establishment used to imperial ways around the world cannot be transformed overnight.

While legal scholars are entitled to dispute a free pass for CIA torturers, they may not realize the sensitivity of the issue of American presidents confronting the entrenched might of the military-industrial complex. Obama is a shrewd operator who has learnt the lessons of the 1960s, when John F Kennedy and Robert Kennedy were assassinated while trying to shake up the national security system. Should Obama endorse full-fledged prosecutions of all offenders from the "war on terror", the infamous system could retaliate with the instrument it knows best - physical violence.

Those impatient for the whole truth to come out and for CIA and US Army officials to be pilloried in broad daylight have to realize that Obama will be cautious and gradualist in downsizing the influence of the Pentagon, the armed forces and their vast panoply of defense contractors, mercenaries ("private military firms") and civilian bureaucrats. No intelligent American president can launch a war against his own state's core pillars in a short period.

The question of grave injustices meted out during the "war on terror" will linger for years to come, but Obama cannot be faulted for not creating the political space in which slow but definite accountability is being restored to the world's most powerful military-intelligence machine.

His objective of halving the US's spiraling budget deficit by the end of the first term of four years could well augur a carefully orchestrated cut in the Pentagon's humungous appropriations and an eventual reining in of the culture of torture and covert operations that took root in the Bush years. Even if all terror warriors are not adequately exposed, Obama is certain to ensure that their ways will no longer taint American foreign policy.

Sreeram Chaulia is a researcher on international affairs at the Maxwell School of Citizenship and Public Affairs in Syracuse, New York.

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