The US homeland security secretary, Michael Chertoff, has insisted the six Guantánamo Bay prisoners accused over the September 11 attacks will be fairly tried, despite concerns about a "show trial".

Military prosecutors said yesterday they would seek the death penalty against the six, including the alleged mastermind of the plot, Khalid Sheikh Mohammed, and the alleged would-be 20th hijacker, Mohammed al-Qahtani, as well as funders of the plot and men alleged to be coordinators between the 19 hijackers and al-Qaida operatives.

The defence department, which is leading the prosecution through a much-criticised process of military commissions, issued 169 charges against the men, including conspiracy, murder in violation of the law of war, attacking civilians, destruction of property and terrorism.

Mohammed, the highest profile of the six, has confessed to being responsible "from A to Z" for 9/11, according to the Pentagon.

Human rights campaigners expressed concern about the interrogation techniques used to obtain such confessions.

The director of the CIA, Michael Hayden, admitted for the first time last week that Mohammed had been waterboarded - subjected to simulated drowning, which is widely seen as torture.

Speaking to the Washington Post, Vincent Warren, the executive director of the Centre for Constitutional Rights, which has represented many of the Guantánamo detainees, said the cases were "essentially show trials".

He said: "They are being used to justify six years of lawlessness and barbarity this government has been doing."

But Chertoff told the BBC there would be "full due process and defence lawyers and all of the fundamental rights that would bring to justice those [who] were responsible for one of the worst war crimes in world history".

Asked whether evidence extracted from waterboarding would be used, Chertoff said: "The judges will decide what's reasonably admissible and what's not admissible."

The announcement of the charges brings to a head the simmering conflict over the legal treatment of the 275 detainees remaining at Guantánamo, and particularly the 15 "high-value" suspected terrorists held since September 2006. Lawyers working on behalf of detainees have long criticised the commissions process – in which even the judges are military personnel - as unfair, unduly secret and against the US constitutional right to habeas corpus.

According to the British lawyer Clive Stafford Smith, who works with Guantánamo detainees, only one of the six men charged yesterday has had access to a lawyer in recent months.

At least two more of the six had been put through "enhanced interrogation" techniques that include sleep deprivation and questioning for up to 20 hours at a time.

All these concerns will be amplified by the decision to press for capital punishment, which is certain to arouse European opposition on those grounds alone. It also presents the Pentagon with logistical problems as there is only one lawyer qualified to prosecute a death penalty case within its military commissions team.

Stafford Smith said the move played into the terrorists' hands. "They want to be martyrs. If we execute them, we fulfil their greatest wish. This is a long process of them getting what they want and that makes us all less safe."

The next stage in the process will be for the charges to be reviewed by a supervising judge, Susan Crawford. She will have to decide whether to allow the prosecution to seek the death penalty.

The charges come at a sensitive time in the tussle over the military commissions. The supreme court heard arguments about the legality of the system last December when opponents argued the removal of habeas corpus from detainees was unconstitutional.

The court, which is expected to give its ruling in a few weeks, struck down the military tribunals in 2006. But the Bush administration responded by passing legislation to legitimise the system.

Amnesty International also expressed concern about the fairness of the trials. Rob Freer, its US researcher, said: "No US citizen would be tried under these military commissions, rendering them discriminatory, in violation of international law.

"The international community must challenge the US to drop these military commissions and conduct trials in front of independent and impartial courts, without resort to the death penalty."

Some relatives of the September 11 victims have welcomed the charges and the possibility of death sentences.

Patricia Bingley, who lost her son Kevin Dennis in the attacks, said: "I believe if there is real evidence that these people had any connection, no matter how small, they should be found guilty. I'm not a bit bothered over how they are going to die."

Diane Horning, who lost her son Matthew, said: "I know my son opposed the death penalty, so I oppose it. It wouldn't be true to his spirit to condone that."