The comments were included in an audio tape released on an Islamist web site, with the voice introduced as al-Zarqawi.
“The killing of infidels by any method including martyrdom operations has been sanctified by many scholars even if it meant killing innocent Muslims,” said the voice.
“This legality has been agreed upon … so as not to disrupt Jihad,” said the voice, speaking in Arabic.
Al-Zarqawi is considered Washington’s most wanted militant in Iraq, and his group is considered to have been behind most of the recent suicide attacks that have killed over 400 people since Iraq’s new government was named last month.
His message appears aimed at winning support from Sunni Muslims for the insurgency.
“Protecting religion is more important than protecting (Muslim) lives, honour or wealth,” said the voice.
“The shedding of Muslim blood … is allowed in order to avoid the greater evil of disrupting jihad.”
There has been no confirmation on whether the voice is indeed that of the militant.
“God knows that we were careful not to kill Muslims and we have called off many operations in the past to avoid losses … but we cannot kill infidels without killing some Muslims. It is unavoidable,” he added.
Chairman of the US’ Joint Chiefs of Staff, General Richard Meyers, told CNN he does not doubt the voice is that of al-Zarqawi.
The tape also said it is crucial to intensify suicide attacks, in order to weaken the military might of the enemy.
There have been 21 car bombings, mostly suicide attacks, in Baghdad and its surrounds in May.
The audio comes as the US military claims al-Zarqawi personally ordered the recent onslaught of suicide bombings, which was organised at a secret gathering of al-Zarqawi and his senior henchmen in Syria last month.
And a British newspaper earlier this week said he was wounded and briefly received treatment at a hospital last week in the western city of Ramadi.
Meanwhile, a senior Iraqi oil ministry official has been shot dead by gunmen in Baghdad.
Police said Ali Hameed was killed outside his home as he left for work.