A Northern Territory Government proposal to introduce legislation that could see pregnant women prosecuted for drinking is facing strong opposition from alcohol research groups and Aboriginal leaders.

NT Attorney-General John Elferink says something needs to be done about the large number of children growing up in the territory with foetal alcohol syndrome.

In an interview with ABC's Lateline on Thursday he said that his government is considering tough new measures that could stop pregnant women from drinking alcohol, including criminal penalties.

"Here in the NT, without pre-empting a cabinet decision, we are currently exploring the antenatal rights of the unborn child," he said.

"Either to prosecute or alternatively to restrain [pregnant women] from engaging in conduct which harms their unborn child."

Opposition health spokeswoman Nicole Manison expressed guarded support for the idea.

"We need to see more detail about what the Government's intentions are," she said.

"It's very early days but by all means we welcome having more discussion about it."

It is estimated that up to 3,000 babies born in Australia each year are suffering from foetal alcohol spectrum disorder, known as FASD, a condition which can leave children intellectually disabled for life.

Foundation for Alcohol Research and Education spokeswoman Caterina Giorgi says that criminalising drinking among pregnant women will not work.

"A proposal like this will deter women who need help from trying to access it and that will cause even greater levels of harm in the future," Ms Giorgi said.

The research group says Australia lags well behind other countries like Canada in dealing with FASD and that education and awareness are the key.

"What we need to do is focus on prevention and encouraging health professionals to talk to pregnant women about their alcohol consumption," Ms Giorgi said.

"We need to ensure there is adequate treatment and rehabilitation for women who are pregnant and alcohol dependent."

Dr John Boffa from the People's Alcohol Action Coalition in Alice Springs says he does not want to see drinking among pregnant women criminalised but he does want the unborn child to be included in the state's child protection act.

"At present the child protection act in the Northern Territory only kicks in once a baby is born and we can't make referrals in-utero," he said.

"When we know that there is a problem and we know there is a woman heavily drinking antenatally and not stopping, there needs to be a way to refer that woman to the child protection system.

"Then the child protection system can take various actions to try and address that."

Dr Boffa says once the unborn child is acknowledged, authorities can take action such as referring individuals for child protection income management.

"There is also the possibility of sending such women to the assessment process in the current Northern Territory alcohol management treatment system," he said.

Aboriginal leaders from Elcho Island off the coast of Arnhem Land say that traditional cultural laws should be used to discipline women who drink while pregnant.

"We need more of the disciplining to be done our way," chair of the Uniting Aboriginal and Islander Christian Congress, Reverend Rronang Garrawurra said.

"We need to control this problem, this issue. We can solve this problem by disciplining our family through our system of justice."