"Newspapers have a great future, I just think they're going through a really difficult period of evolution.
"It's the fastest and biggest evolution that they've ever undergone in their long history. And I think they will come out of it in two or three years."
Mr Thomson, now executive chairman of digital agency Nation 1, said he believed that by 2020, newspapers would emerge as a more valued and trusted medium than at any time in the past 50 years.
He realised that view put him out of step with some media commentators who believed current declines in revenue in the industry were irreversible.
But now papers around the world were actively promoting and improving their offline and online content and working out how to make money from it.
Mr Thomson said the Herald's relaunch of size and content, with the first compact paper out on Monday, was a good example of such adaptation.
"When the Times did it it was unbelievably controversial. But so long as the product's good, consumers are incredibly adaptable.
"Newspapers stood still for nearly 50 years. And they will never do that again. I think now newspapers will continually evolve."