The move follows a decision by Peter Peacock, the education minister, to allow state schools to merge the subject with others in the early years of secondary.
Lochend Community High and Govan High, both in Glasgow, are to phase out the subject for first and second-year pupils from next year.
Last week members of the Scottish Association of Teachers of History met MSPs to voice fears for their subject.
Fiona Valpy, assistant director for the Scottish Council for Independent Schools, said: “Independent schools will be keeping history as a separate subject on the curriculum. There has not even been a debate about getting rid of it or teaching it in classes along with other subjects.
“History always has a very good uptake and is a popular and strong part of the curriculum in independent schools.”
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David Girdwood, rector of St Columba’s school in Kilmacolm, said state schools which dropped history were short-changing their pupils.
“I expect many of my pupils to enter the professions and hold posts of leadership and responsibility,” he said.
“They will be decision makers, they will need to demonstrate vision and they could not possibly do that without any understanding of the past,” he said.
Colin Mair, headmaster of the High School of Glasgow, said history remained an important part of the curriculum.
The head teachers of Lochhead Community High or Govan High school were not available for comment. A spokeswoman for the council said it was “up to individual schools” how they would deliver the curriculum. “The council will monitor how this is being done,” she said.