John Reid has urged people to give UK troops more support and be "slower to condemn" them as they take on an enemy "unconstrained by morality".
The defence secretary said forces were on an "uneven battlefield", because of the "scrutiny, accountability, media intrusion and questioning" they face.
By contrast the enemy was not hindered "by any legitimacy, any morality, any international convention", he said.
"Let us be very slow to condemn our troops, our forces," he told BBC radio.
Mr Reid spoke out after he signalled that UK forces could soon begin their withdrawal from Iraq, and days after announcing the deployment of more troops to Afghanistan.
The UK has about 8,900 personnel stationed in Iraq, mainly in the south east.
Mr Reid told BBC Radio 4's Today programme there had to be a balance between the scrutiny cast upon British troops and the enemy they faced.
"We can't continually have an uneven battlefield for our troops, where we are facing an enemy, unconstrained by any legitimacy, any morality, any international convention and at the same time, subject our troops to a level of scrutiny, accountability, media intrusion, questioning and every conceivable opportunity to criticise them," he said.
"I say in that kind of world, where we are facing that kind of enemy, let us be very slow to condemn our troops, our forces, and very quick to support and understand them."
On Tuesday, Mr Reid said conditions in the region were "well on the way" to being suitable for a withdrawal of UK troops.
He said "significantly fewer" service personnel could be posted to the country next year but added that the government would not "cut and run".
Iraqis wanted troops to leave "just as soon as the conditions are right", Mr Reid said in a speech in London.
Last week, Corporal Gordon Pritchard became the 100th member of the UK armed forces to die in the conflict.