Alfred Baird, professor of maritime business at Edinburgh Napier University, said Scottish higher education is dominated by university leaders who are not born here – with only four of 15 universities led by Scots.
He added Scottish academics were also a "rapidly diminishing species" as universities recruit staff from across the world.
In December, leading author and artist Alasdair Gray was criticised after attacking English "colonists" who hold influential jobs in Scotland.
Although his comments were directed at the arts, he said "other professions will know settlers and colonists with similar attitudes".
Writing in the online magazine Scottish Review, Mr Baird made reference to Mr Gray's essay saying the diminishing role of senior Scots academics was clearly evident.
"If Scots did so much to invent this and that and the next thing, how come we are no longer rated competent enough to lead and manage our own nation's universities? What does that say about the Scots?" he asked.
"I think most Scots will agree that it would indeed be a sorry state of affairs if Scots were no longer leading any of Scotland's universities, yet this is not far from the reality today, and the trend is rapidly heading towards that outcome."
Mr Baird said Scots academics were fast becoming a minority in many teaching departments and research centres within Scotland's universities and said this impacted on the relevance of research work to the country.
"With much of the research undertaken by academics coming from countries outside Scotland, they might be forgiven for not bringing with them a personal priority or interest to research matters of importance to Scotland," he said.
"With senior Scots academics increasingly a minority within Scotland's universities, this leads to a loss of distinctiveness as well as the likelihood that a primary focus on Scotland is not being prioritised. Universities in other nations do, of course, recruit talented academics from elsewhere, but not to anything like the extent Scotland has done. Scotland's universities have been virtually overrun, swamped by comparison."
However, a spokeswoman for Universities Scotland, which represents university principals, dismissed the concerns.
She said: "The development and cultivation of Scottish talent is an essential element of our university sector, we do not accept for a moment that only Scottish principals are able to take this responsibility seriously.
"All our universities compete and succeed on a global stage. The international mobility of academic staff and ideas is a key ingredient of this success.
"Universities have an important role in producing graduates with a modern, international view of the world, and should resist insularity and parochialism. Delivering for Scotland in return for the public investment universities receive is a priority for every one of the principals of Scotland's universities, irrespective of where they were born."