The depiction of the bird will have been the last thing some people saw before being "marched to their deaths", Jackson Carlaw said.
An eagle was used with a swastika by the Nazis, as well as a symbol by the Roman legion.
"The golden eagle is the symbol of a empire that once invaded large parts of Scotland, and more recently of another empire that tried to," Mr Carlaw said.
"In the lifetime of many people in this country it was the last thing their relatives saw as they were marched to their deaths.
"It has been a symbol of imperial power of which Scotland is emphatically not, never has been, and hopefully never will be.
"Is an eagle - the symbol of imperial authority - the right national symbol for a democratic nation like Scotland?"
A "tenacious" robin would be a better symbol, he suggested.
Mr Carlaw spoke out as MSPs on the Public Petitions Committee considered a call to make the golden eagle the national bird.
The petition was put forward by RSPB Scotland with support from wildlife cameraman Gordon Buchanan.
The film-maker later rejected Mr Carlaw's concerns.
"He's making a contentious point but I don't think if the symbol was shown to people in Scotland as the national bird, that anyone would see it as Nazi," he said.
The RSPB says there are 431 pairs of golden eagles in Scotland. Persecution of the birds mean they are confined to more remote areas of the country, the body says.
Mr Buchanan hopes formal designation could improve eagle numbers.
"Speaking to colleagues that I have south of the border, people that have an appreciation for wildlife, they are absolutely astounded that this persecution, poisonings and shootings of golden eagles continues," he told the committee.
"Giving it the status of Scotland's national bird will help protect it further."
Before the meeting, Stuart Housden, director of RSPB Scotland, said: "The majestic sight of a golden eagle soaring effortlessly above the treetops, or along a dramatic cliff edge, never fails to impress, so much so that this spectacular species was recently named Scotland's favourite animal following a public vote.
"What better legacy can we provide for this initiative than to officially designate the eagle as Scotland's national bird and join together for its future conservation?
"It would formally recognise the place this species has unofficially occupied in our culture for many centuries and show our commitment and desire to protect and conserve it, and our wider national heritage, for generations to come."
MSPs agreed to ask the Scottish Government to consider whether to hold a formal consultation on the proposed national bird.
The petition is the 1,500th lodged with MSPs on the Public Petitions Committee.
A consultation has already been held in Scotland on whether to adopt a national tree.