The skull, which was expected to sell between £500 and £700, was withdrawn from a sale at Ramsay Cornish Auctioneers in Leith.
It is believed the skull was recovered from a Victorian-era excavation somewhere in the Durham area.
Dr Simon Gilmour, director of the Society of Antiquaries of Scotland, contacted the auctioneers on Friday to raise concerns about the skull which was due to be sold on Saturday.
He said he wanted to work with all auction houses to stop the sale of human remains. While not illegal to do so , Dr Gilmour said such sales raised ethical and moral issues.
Dr Gilmour credited the auction house for removing the item.
He said: The key thing herd is that selling such an item is legal – that is the core thing. There is a blind spot where human remains are concerned. You cannot own a human body or remains so we find it odd that you can sell them.
"It is a grey area and it is one that we want to tackle and close the loophhole.
"For us, it is an ethical issue. You are talking about part of a human body, a person, someone’s son or daughter and it should be treated with respect.
Dr Gilmour said archaeologists and those working with human remains were bound by a strict code of ethics with disturbed remains to be be reburied following analysis.”
He added: “If remains end up being sold, then it is very unlikely that it will be re-buried.”
The Society said it supported British Association for Biological Anthropology and Osteoarchaeology (BABAO), who said the sale of human remains is unethical.
BABAO said there have been “numerous cases” in recent years where human remains have been bought and sold for financial gain.
A statement said: “ It is ethically objectionable to commodify the remains of people as objects, and the concept of ‘ownership’ of most human remains is not recognised in law. “
It said there was a “wider concern” that trade encouraged looting of both archaeological and contemporary burial sites.
A spokeswoman for Ramsay Cornish Auctioneers said the item was removed soon after contact was made by Dr Gilmour.
She added: “The skull came from a dig, a burial site, and that is why we wanted to remove it. A skull which comes from a medical provenace might be viewed differently.
"It is very delicate territory but I am comfortable with the decision. There is a lot of censoring of objects and there are debates to be had, with each side listened to. Some might question whether it is legitimate to excavate a burial site. The reality is these are very important issues.”
A skull which belonged to the Edinburgh artist Sir William Mactaggart and which was used as a studio prop fetched £900 at the auction house in December. A market existed among those with an interest in the macabre, as well as oddities and curiousities, the spokeswoman added.
The spokeswoman said: “Our leaning would be not to include any more skulls until a wider debate has been had."