Maliki, speaking in Cairo during a state visit, said the wall reminded people of "other walls," The New York Times reported.
"I oppose the building of the wall, and its construction will stop," Maliki said during a news conference with Amr Moussa, the Arab League secretary-general. "There are other methods to protect neighborhoods."
U.S. spokesman Lt. Col. Christopher Garver said the military would continue talking with the Baghdad government about the best approach to protecting the public. The military did not say whether construction on the wall would be stopped, the newspaper said.
Maliki did not specify which "other walls" he was referring to, but the Times noted that the separation barrier Israel is erecting in the West Bank is a delicate issue among Arabs. Israel says the barrier is for protection, but the project has angered many Palestinians.
The wall under construction in Baghdad would set off a Sunni Arab neighborhood that is a frequent target of mortar attacks and incursions from Shiite neighborhoods that surround it, the Times said. It has also been used by militant Sunni Arab groups as a stronghold.