The BBC's Panorama programme reported coalition and Iraqi security forces were responsible for most civilian conflict deaths in the past six months.
But the health ministry says that its figures were misinterpreted.
"The BBC regrets mistakes in its published and broadcast reports," said a BBC spokesman.
This BBC item goes on to explain:
"The BBC regrets mistakes in its published and broadcast reports," said a BBC spokesman.
The Iraqi figures said that 3,274 people died in conflict situations in the period July-December 2004.
Of these, 2,041 of those were categorised as the result of "military operations" while 1,233 were blamed on "terrorist operations".
But the health ministry says those recorded as dying in military action included people killed by insurgents, not just those killed by troops from the multinational force or Iraqi security bodies.
The deaths recorded included those of militants as well as civilians, officials said.
