The Royal College of Midwives said the plot, involving the characters Honey and Billy Mitchell, was unrealistic and would worry expectant couples.
The RCM is angry Honey was shown being refused an epidural when in pain, and being told about her baby's condition without her husband being present.
But a BBC spokeswoman said the scenes were based on real-life experiences.
A spokeswoman for the RCM said: "What the soaps do is set scenes which prompt people to talk about things which are affecting their lives.
"We are concerned people will wrongly think this Down's syndrome story shows what really happens, and that if you have a problem there is no one there to support you."
"Showing something like this is not helpful."
But a spokeswoman for the BBC said it had been preparing for the storyline since the beginning of the year, talking to families with children who have Down's syndrome and a midwife from a major hospital about the storyline, as well as the Down's Syndrome Association.
She added: "EastEnders has in fact drawn directly from one particular true-life story.
"And while this may indeed not be best practice, it is worth saying that good drama does not necessarily come from best practice."
Carol Boys, chief executive of the Down's Syndrome Association, said: "The way in which Billy and Honey have learnt of their baby's disability, and their subsequent support from their health professionals, is not a best practice model.
"However, neither is it an unrealistic situation."
She cited research carried out this year which found nearly 40% of parents who have a child with Down's syndrome whose condition is diagnosed after the birth are given no written or practical information about the condition.
Ms Boys added: "Some health professionals hold outdated or prejudiced views about people with Down's syndrome that prevent them from giving parents a balanced picture of what the future will hold for them."