Two charities, the British Pregnancy Advisory Service (Bpas) and Birthrights, said the case was of "profound social significance" and said any legal developments that "call into question a pregnant woman's fundamental right to bodily autonomy" should be taken "very seriously".
There are fears it could mean other aspects of women's behaviour - such as medication taken during pregnancy or her choice of childbirth - could also have damning implications.
Charities also fear women with addictions could choose to abort their unborn children rather than face criminal prosecution.
Ann Furedi, chief executive of Bpas, and Rebecca Schiller, co-chair of Birthrights, said: "Making one particular form of behaviour during pregnancy into a criminal offence would lay the ground for criminalising a wide range of other behaviours because they may too pose a risk to the health of the baby."
Similar developments in the US have resulted in women being imprisoned.
The National Advocates for Pregnant Women in the country has urged caution over this case. It has called on the court to "reject efforts to create criminal penalties as a mechanism for addressing health problems women may face during pregnancy".
In the case, to be heard this week, the girl was born with fetal alcohol syndrome, which can cause stunted growth, facial abnormalities and intellectual impairment.
The syndrome was diagnosed 252 times in England between 2012 and 2013.
But the charities claim that there is "continuing uncertainty" in the medical profession over the relationship between drinking and harm to the fetus.
And they say mothers and their babies would not be best served by treating pregnant women with drug or alcohol abuse problems as criminals.
Lawyers representing the local authority are seeking to prove the 6-year-old's mother committed a crime under the Offences Against the Person Act 1861.
Neither the girl nor the mother was identified in the ruling.
3 facts on fetal alcohol syndrome
1 Fetal alcohol syndrome is a complex condition, denoting a collection of features including retarded growth, facial abnormalities and intellectual impairment.
2 There remains uncertainty in the medical community over the relationship between alcohol consumption and harm to the fetus.
3 While it occurs in babies born to alcoholic women, most babies of alcoholic women will not be affected as other factors, including nutritional status, genetic makeup of mother and fetus, age and general health, are also thought to play a role.
- Daily Mail