An investigation found doctors at Glasgow's Southern General put under the woman under, "extraordinary pressure" to take preventative antibiotics to protect her unborn baby from infection.
The woman was told by medics they would obtain a child protection order from the courts which would apply when the baby was born.
However, the report was critical of the doctor's conduct because the situation was not "life-threatening".
NHS Greater Glasgow and Clyde has been ordered to apologise to the patient and to hold a review into the case.
The woman was advised by medics to take antibiotics because she had a ruptured membrane which can cause an infection in the mother and baby.
She agreed with a doctor that she would not take the pills but her baby would be monitored for signs of infection after the birth.
However, a second consultant disagreed with the decision and told her they would obtain a child protection order if she did not take the antibiotics.
The woman agreed because she was afraid they would take her baby away.
An investigation by the Scottish Public Services Ombudsman concluded that the woman should have been allowed to decline the antibiotics.
The report said: "The failures by the Board led to a significant personal injustice to Ms C.
"She did not properly consent to the treatment administered and was wrongly put under extraordinary pressure during labour when she was in a very vulnerable situation.
"This was not a life threatening situation and Ms C's preferred management strategy was acceptable under the Board's guidelines."
A spokeswoman for NHS Greater Glasgow and Clyde said: "We have received the Ombudsman's Report and fully accept that in this case there were lessons to be learned from this patient's experience.
"We have initiated a number of actions to improve communications between staff and patients, particularly when sensitivity and empathy are expected.
"We have already apologised to the patient and will do so again."