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Dr Caroline Gannon investigated the deaths of babies including those in the womb or stillbirths.
She said the final straw was having to advise a couple to use a picnic cooler bag to return their baby's remains to NI following an abortion in England.
The attorney general said the law was under consideration.
A family can have a post-mortem examination carried out in England - but they are difficult to arrange.
Dr Gannon's resignation leaves Northern Ireland with only one paediatric pathologist.
She said the recent interventions made her position "untenable".
"I think he (the Attorney General John Larkin) was the tipping point," she said.
"The workload we had was manageable, but then when these rulings came out - that was the tipping point and for me, professionally, I just felt I was acting unethically by taking part in this system where parents are denied a voice in what happened to their baby."
AG's interventions in NI abortion law:
Dr Gannon cited the example of one couple who wanted a post-mortem examination to find out why they had been told their baby had a fatal foetal abnormality.
As it remains illegal in Northern Ireland for an abortion to be carried out on the grounds of such a diagnosis, the couple had to travel to England for a termination.
The only way they could find to transport the remains home was in the cooler bag with ice packs.
"They're on their own in a strange town, a strange country in a private clinic with no support," said Dr Gannon.
"If this had happened in a hospital in Northern Ireland midwives would be there, hospital processes would be in place they could sit with their baby and then somebody else would be responsible for bringing their baby down to the mortuary to ensure the post mortem is carried out.
"But they were on their own and they had to organise that themselves and transport their own baby's body back in a picnic cooler in the boot of the car on the overnight ferry."
Attorney General statement
Mr Larkin previously argued that allowing terminations in cases of fatal foetal abnormality discriminates against children with disabilities. He has also said there is no agreed clinical definition of fatal foetal abnormality.
The BBC understands that several couples have used various modes of transport including a parcel courier company to carry the remains of their baby home.
Dr Gannon, who has worked in Northern Ireland for almost 30 years, said she feels it's "unethical" to work in a system where women and couples are being "denied information and choice".
"I just cannot work in this particular system. I find it very difficult and I cannot reconcile the legal system I am having to operate under with my own personal ethical beliefs."