A brief statement on Wednesday from the joint Iraqi-US security body named the victims as Saleha Mohammed, 55, and Nabiha Nasif, 35.
The Joint Coordination Centre statement said, without specifying if either of the women was pregnant: "US forces killed two women by mistake ... when they were heading to a maternity hospital in a taxi."
A police source said the driver of the car was wounded.
The US military said a car had entered a clearly marked prohibited area near an observation post.
Lieutenant Colonel Ed Loomis said in a statement: "As the vehicle neared the observation post and failed to stop despite repeated visual and auditory signals, shots were fired to disable the vehicle.
"The vehicle stopped, changed directions and quickly departed the area."
He said the military later received Iraqi police reports that two women had died from gunshot wounds at the hospital in the town of Samarra, 100km north of Baghdad.
"The loss of life is regrettable and coalition forces go to great lengths to prevent them," he said. "The incident is under investigation."
The news of the deaths came a day after Nuri al-Maliki, Iraq's prime minister, said his patience was wearing thin with "excuses" from US troops that they kill civilians by mistake.
The US military is also under pressure over revelations that US marines may have killed 24 civilians in the town of Haditha during an unprovoked attack last November.
Ordinary Iraqis complain that US soldiers manning checkpoints are too quick to open fire at approaching vehicles, often resulting in the death of civilians.