The officer, who last week resigned from the Army, said: “It’s very hard to give legal advice that contradicts the government line they [superiors] wish to be taken.
“I think the millions of pounds that are spent by the Ministry of Defence trying to extract itself from the European Convention of Human Rights was extraordinary.
"It's an absurd position – and in fact what's wrong with giving people human rights?"
Lt Col Mercer claims he first encountered resistance from superiors when he warned the Army was breaking the law by failing to individually assess detainees to separate civilians from prisoners of war.
“We were convening tribunals of 250 prisoners at once,” he said.
“My lawyer there objected to this because it was patently wrong in law and was threatened with being sacked unless he changed his legal opinion within 24 hours.
“I was threatened with being sacked. I stopped it and then we sorted it out. However, at the same time, while I was down at the prisoner of war camp, I went past the interrogation facility and saw the prisoners hooded and in stress positions.”
Mercer said this breached the Geneva Convention and subsequently attended a meeting with military commanders and members of the British Red Cross, who had also raised similar concerns.
“I was prevented from speaking at that meeting by the Ministry of Defence”, he said.
He also claims that the MoD ignored his warnings that Britain was obliged to comply with European human rights law in its treatment of prisoners in Iraq after it legally became an occupying power.
“Like all prisoners held by the United Kingdom, as soon as you’re arrested, the clock starts running. You’re entitled to know the charges against you, you’re entitled to have legal representation, and you’re entitled to have a review of your case.”
He claims that superiors unequivocally rejected his advice, insisting the European convention on human rights did not apply in Iraq.
The European Court this year ruled that the convention on human rights did apply to prisoners in Iraq.
Lt Col Mercer, whose career was left in tatters after becoming an outspoken critic of the tactics employed in Iraq, has spent the last three years training as an Anglican cleric and was ordained last week.
He openly condemned the Army’s treatment of prisoners in his evidence to the Baha Mousa inquiry, disclosing that eight or more civilians were died in the custody of British forces in the weeks following the invasion or Iraq.
Lt Col Mercer warned that aggressive forms of interrogation still practised by the Armed forces – known as “harshing” – are also illegal and condemned Defence Secretary Liam Fox for defending its use in certain circumstances.
Lt Col Mercer accused the MoD of “moral ambivalence" about Britain's human rights obligations.
Responding to the claims, an MoD spokesman said: “The Chief of General Staff, General Sir Peter Wall, has already apologised for the loss of discipline and lack of moral courage that occurred in Iraq and this remains a stain on the Army’s reputation.
"All British troops now undergo training in international humanitarian law and other rules relating to the conduct of hostilities and the implications for conducting operations in difficult and dangerous circumstances.
"This training underpins all our detention policy, and in Afghanistan, where detaining and interrogating key insurgents is critical to our mission, high standards are in place and adherence to them is rigorously monitored.”