Maliki's statement referred to a raid Sunday in the predominantly Shiite area of Sadr City, a New York Times (NYSE:NYT) correspondent reported Monday.
U.S. forces staged a raid searching for a suspect in an allegedly Iranian-backed kidnapping ring and, in three locations, were met with heavy fire from insurgents.
The military said in a statement at least 33 people were killed by ground fire in the initial engagement and six others by air attacks, followed by 10 others as U.S. troops withdrew.
Counter to Iraqi witnesses' claims, the military said only insurgents were killed.
"Ground forces reported they were unaware of any innocent civilians being killed as a result of this operation," the military statement said.
Area hospitals said 40 people were being treated for injuries and a number of children were among the victims, the report said.