Conservative MSP Jackson Carlaw has attacked a proposal to make the eagle a national symbol of Scotland, recalling its use by the Roman empire and later by Nazi Germany.
Mr Carlaw sits on a Holyrood committee considering a petition to make the golden eagle Scotland's national bird.
He suggested the eagle was a symbol of "imperial power".
Wildlife photographer Gordon Buchanan, who backs the petition, denied any Nazi links.
The Scottish Parliament's public petitions committee questioned Mr Buchanan and RSPB Scotland's Duncan Orr-Ewing.
Mr Carlaw said: "The golden eagle is the symbol of an empire that once invaded large parts of Scotland, and more recently of another empire that tried to.
"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."
Mr Carlaw said the robin would be a better national bird, but wondered why another national symbol was needed at all and where such thinking would end.
"Do we have a national domestic animal, a national wild animal, a national grievance?" he asked.
Later Mr Buchanan said he doubted "if the symbol was shown to people in Scotland as the national bird, that anyone would see it as Nazi."
The petition was lodged in December by RSPB Scotland director Stuart Housden. It calls for the golden eagle to become a national symbol", alongside the lion rampant, Saltire and Scottish thistle as emblems of the country".
Mr Orr-Ewing said the golden eagle was a "true bird icon of Scotland", arguing that many highland chieftains wore an eagle feather, as did Scottish regiments and the Royal Company of Archers.
He said Scotland's golden eagle population "represents the whole of the UK's breeding pairs, and it is regarded as a Scottish species".
RSPB Scotland has said there are only 431 pairs of golden eagles remaining in Scotland, as a result of what it calls "centuries of persecution".
Mr Buchanan said colleagues of his elsewhere in the UK were "astounded that this persecution, poisonings and shootings, continues".
In December, police appealed for information after tests revealed a golden eagle found dead in Angus had been poisoned.
A recent report by RSPB Scotland revealed that a significant number of incidents of illegal killing of birds of prey took place in areas managed for grouse shooting.
Last year, the golden eagle topped a poll in a campaign by Scottish Natural Heritage and VisitScotland to find Scotland's favourite wild animal, as part of the Year of Natural Scotland 2013 celebrations.
The petitioners are hoping that the eagle will follow the Scots pine as a national symbol. The Scots pine is to be designated Scotland's national tree following a petition to the Scottish Parliament from campaigner Alex Hamilton.
The committee resolved to put the golden eagle proposal to consultation, as had previously been done with the petition on the Scots pine.
Committee chairman and Labour MSP David Stewart confirmed that he and his colleagues were "taking this forward".